PhD Thesis Handbook

This thesis handbook is for the PhD students for Health Systems Research and Health Professions Education Research program.


PhD Major Milestones

  1. Coursework
  2. Comprehensive course and exam
  3. Form the committee (can happen before comprehensives)
  1. Proposal defence
  2. Submit protocol for Research Ethics Board (REB), review and approval (approval may take several months, can do scoping reviews while waiting for REB)
  3. Research and writing
  1. Final oral exam (FOE)
  2. Modifications and Thesis Submission

Supporting Activities

  • Intake meeting (Memorandum of Agreement (MOU) plus forms for annual review meeting forms)
  • Annual review meeting (emphasis lead and supervisor) and form and financial declaration of employment and awards
  • Meeting with the committee (at least two times annually) [or equivalent communication about thesis progress]
  • Publishing your work 

Selecting a Suitable Thesis Topic  

Purpose of a PhD Thesis

The PhD thesis is an original piece of scholarly research. It is a major undertaking that reflects the highest standards of scholarship and makes a significant contribution to knowledge and practice in the field of health systems research. PhD research is one in which there is an element of originality (the work represents a unique contribution to the field) and either the potential for three published papers as a result or an equivalent amount of work. The thesis research is conducted under the guidance of a supervisor and in consultation with the thesis research committee.

Introduction – The PhD Thesis

Although courses are an important part of the PhD program, it is the research and thesis writing that provide the main opportunities for developing both a broad perspective and in-depth knowledge of a particular area of research.

Earning a PhD degree is more than simply completing a few courses, carrying out a piece of research and writing a thesis; it is the process of becoming a well-rounded researcher in health systems research or health professions education research: one that is knowledgeable about theory, methodologically rigorous, and can make a real-life impact. The PhD thesis demonstrates a wide, critical knowledge of the field; an ability to ask appropriate questions and set the research in its proper context; that the appropriate research methods have been mastered; and that the ideas and results are communicated effectively. It is about making an original contribution to a particular research field within a framework of research training. ‘Original contribution’ means finding a gap in knowledge and answering a question posed by that gap.

Selecting a Research Topic

There are many suitable topics for research in Health Systems Research and Health Professions Education Research. The selection of a research topic should be the result of a consultation between the student and supervisor. A good research topic is one that:

  • Addresses an important real-life problem;
  • Fills in gaps in current knowledge and understanding;
  • Relevant to the field of HPER or HSR, and your emphasis (for HSR);
  • You are passionate about and interested in.

Ideas for research topics may come from many sources including your past studies, readings, and perhaps most importantly, personal experiences. By the time you are admitted into the program, you should have already formed a general idea of your thesis topic.

While it is important for the topic to be within the general research area of your supervisor, it is not necessary for the supervisor to be an expert in the specific topic. By the time you finish your PhD, you should become an expert on that topic.

Review Past IHPME Thesis Topics

Selecting a Supervisor / Role of the Supervisor

Selecting a Supervisor

All PhD students are required to find a supervisor who will act as a mentor and guide as they proceed through their degree.

The choice of a faculty member who will supervise the thesis work required to fulfill degree requirements is one of the most critical decisions a graduate student will make and should not be taken lightly. A student will need not only a competent supervisor in a particular area but also willing to act as the student’s advocate when necessary. It is important that the student be able to work and communicate effectively with the supervisor and not feel overwhelmed or intimidated in the relationship. Each student requires the guidance of someone who will stimulate thoughts, who has sufficient interest in the student’s topic to produce insights jointly, and who will challenge the student to think in a novel manner about the research.

The following suggestions are included to help students find an appropriate supervisor:

  • Look through the list of IHPME Faculty and Research and Initiatives on the IHPME website to find a professor that fits you by:
    • Emphasis they are affiliated with
    • Content expertise
    • Methodological expertise

(You are NOT restricted to content – someone out of your area with a “method” match can be great!)

  • Ensure that your potential supervisor has the appropriate SGS appointment level: PhD students need a supervisor who is a Full SGS member. If you are interested in working with a supervisor who does not have this level of appointment, you may discuss it with them. They may suggest someone with the appropriate SGS appointment level and/or may serve as a co-supervisor.
  • Students may get to know the potential supervisor whose research interests parallel their own. Consider doing a database (ProQuest, PubMed, Scopus [2]) search to see what they have published and read some of their recent publications.
  • If possible, talk to other trainees. They will tell you who is a good supervisor. Graduate students working with a specific supervisor are an invaluable source of information.
  • There are tradeoffs in picking a supervisor by seniority/eminence. A very experienced supervisor may help “fast-track” your career. On the other hand, a senior person may not have a lot of time for you.
  • A supervisor is also a mentor, often for the first few years of your career. Someone who is a good mentor can be really helpful.
  • Don’t be afraid to approach potential supervisors cold, i.e., without any personal connection or contact. They expect it. It’s their job (usually among many others) to teach and mentor students.
  • HSR: You may contact the emphasis lead of your area of interest for suggestions

For more information visit:

Role of the Thesis Supervisor

  1. The supervisor provides advice on all aspects of the thesis project. Specifically, they are responsible for providing direction to the student, advice on data sources and potential avenues of approach, instructions on the proper content and form of the thesis, review of the student’s progress, and serving as the first reader of the thesis. It is the responsibility of the supervisor to help the student think through conceptual and methodological issues and to raise questions about possible decisions faced/taken by the student.
  2. The supervisor and student are expected to read and sign a Memorandum of Agreement (Student-Supervisor MOU) [PDF] before undertaking thesis work. In HSR, this MOU should be submitted to the emphasis lead at or before the intake meeting in the summer before the start of the program.
  3. The supervisor and student are expected to meet on a regular basis at a mutually agreed schedule (many supervisors meet with their students on a bi-weekly basis, but frequency may change depending on need and the stage of the research).
  4. Additionally, the supervisor, in conjunction with the student, is expected to complete annual progress reports, annual statement of employment and awards, and meet with the emphasis leads/program directors to discuss it.

For more information:

What to Do if You Have Challenges Working With Your Supervisor:

  • First, try to discuss it openly with your supervisor. Share your concerns and try to reach mutual agreement.
  • If that doesn’t work, you may contact the Emphasis Leads (HSR) Program Director or Graduate Coordinator
  • Contact the Centre for Graduate Mentorship & Supervision (CGMS) for expert advice

Selection of the Thesis Committee  

Purpose of the Thesis Committee  

The thesis committee gives meaningful input into the thesis proposal and supports you through the research to completion and defence of the PhD thesis.

PhD Thesis Research Committee

The thesis committee should have a minimum of three members (including the supervisor).   In consultation with the supervisor, the student selects two or more additional members for their committee. In the case of co-supervision, only one additional member is needed. Students and supervisors are encouraged to form a committee that can properly support the student, both methodologically and in content expertise.

  • The supervisor, who functions as the Chair of the thesis research committee, must have a full membership to the School of Graduate Studies (SGS) and an appointment through IHPME. See “IHPME Requirements to be a Supervisor” for additional requirements.
  • Committee members are chosen on the basis of their expertise in the student’s area of research and must have a graduate faculty membership (GFM).
    • Committee members can have a graduate faculty membership (full or associate membership with SGS) elsewhere within the University of Toronto, these faculty do not have to apply for an appointment with IHPME.
    • Clinical faculty with appointments elsewhere in the university that do not have a GFM need to apply for it through IHPME. They can send their CV to and will receive the details and a link for the application submission.
    • It is possible to appoint a committee member from outside the university. In this instance, the supervisor must obtain a copy of the outside member’s CV and forward it to the IHPME Appointments Officer who will explain the application process to obtain the GFM.

When all committee members have been selected and have agreed to serve, the Step I (Committee Confirmation) form should be completed by the student, signed by the student and supervisor, and submitted to the Graduate Assistant. This information will be placed in the student’s file. 

Thesis Proposal Approval Process

PhD Thesis Research Proposal

The thesis research proposal is developed with the supervisor and the supervisory committee in a series of iterative steps. Normally the committee meets to discuss the thesis research project generally, after which, drafts of the proposal are submitted to the supervisor and committee for feedback and revision.

The thesis research proposal is usually 20-30 pages in length, double-spaced, excluding references. In consultation with your supervisor, you may write a longer proposal and then shorten it to the required length for the proposal defence. This longer version may serve you later as the basis for some of the chapters of the final thesis.

In developing the research proposal, students should consider the format of the thesis. The two formats used in IHPME are Traditional Thesis and Publication-Based Thesis. The proposal should contain the following elements:

  • Title: The title should give a clear indication of the topic being studied.
  • The Problem: The proposal should contain a description of the study problem which includes specification of the study question(s), justification for their selection in relation to previous research and to the literature, and the potential relevance of the research findings.
  • Theoretical Framework and Background Information: Following a concise and critical review of the theoretical and research literatures, the proposal should discuss the major theoretical premises and the salient concepts which underlie the problem or question(s).  The proposal should then outline a framework, based on literature, for analyzing the problem and question(s).
  • Design and Methods (some aspects may vary depending on the nature of the study): The type of research design should be clearly explained (e.g., survey, descriptive, interpretive, experimental, etc.) as should the reasons for selecting it, including its merits and limitations. The questions and/or hypotheses for the thesis research are formulated clearly. Sampling and recruitment procedures should be clearly outlined, including theoretical and practical reasons for selecting the population or database from which the sample is to be drawn. Sample size, or details of any database, should be included. Data collection methods should be described in detail as should their relationship to the theoretical and conceptual issues associated with the thesis research project.  The methods of analysis appropriate for the study design should be fully described and justified, including their strengths and weaknesses. The proposal should be clear about any conceptual or theoretical issues relating to the analysis of the data.
  • Research Plan (timeline): The proposal should include a detailed plan, with estimates of time needed to complete each phase of the proposed research. Alternatives should be outlined for those elements of the plan which may prove problematic.

Proposal Approval

Once the supervisor and committee approve the proposal:

  • The supervisor and/or committee identify an external examiner. The external examiner must be external to the student’s committee, and possess expertise in an area related to the thesis research.  For the proposal, this can be someone within the University of Toronto, ideally outside of IHPME.    
  • The supervisor/committee must get the CV of the external examiner.
  • The student or supervisor submits the proposal defence form and the external examiner’s CV to the program’s graduate assistant a minimum of six weeks before the anticipated proposal defence date.
  • The external examiner will be reviewed by the graduate coordinator for approval.
  • Once the external examiner is approved, the supervisor or the student must send the research proposal to all members of the proposal examination committee including the external examiner at least four weeks prior to the meeting
  • The graduate assistant will secure a chair for the defence and notify the student and committee as soon as possible.

Proposal Assessment Criteria (see below) are provided to each reviewer and are intended to serve as guidelines for the assessment.

The Proposal Defence

You should schedule 2 hours for the proposal defence. There must be at least 4 voting members present, including the external examiner. During the proposal defence, the student presents a brief summary (20 minutes max) of the thesis research proposal to the examination committee, followed by one or two rounds of questions and responses. Each committee member gets approximately 10 minutes to ask questions in the first round. 

The student then leaves the room and the examination committee votes on the proposal with the following options: 

  • Approved (with a note of decisions regarding additional material and/or analyses to be included in the thesis that were not in the proposal) 
  • Not approved (specify reason, and conditions to be fulfilled prior to re-examination. Date of reconvened examination (must be within 1 year)

The supervisor is responsible for recording the discussion and recommendations and revisions. Following the meeting, the supervisor is responsible for meeting with the student to discuss revisions recommended during the proposal approval meeting.

Research Proposal Assessment Criteria

The following criteria are to be considered by the supervisor and proposal examination committee members in adjudicating the merits of the student’s proposal.

  1. To what extent is the research question focused and researchable?
  2. To what extent is there a coherent and relevant review of the literature in support of the research question?
  3. To what extent are the design and methods appropriate and clearly articulated? Are sampling and recruitment strategies and other sources of information well thought out and appropriate? Are the variables clearly described and their operational definitions outlined  (in quantitative research:)? Are the planned analyses appropriate?
  4. Is the proposal work plan feasible?

The student can proceed to collection of data and preparation of their thesis research ONLY AFTER APPROVAL of their proposal has been obtained from the Approval Committee and only after Ethics Approval has also been obtained.

Submission of Thesis Project for Ethics Review

In accordance with the Tri-Council Policy Statement: Ethical Conduct for Research Involving Humans – TCPS 2, all students conducting research that involves human participants (or data collected from them) must obtain University of Toronto research ethics approval for their research in addition to any approvals required by other institutions such as those of research sites or the home institutions of their supervisors. Note that depending on the research site, risk level and other factors, ethics approval may take several months.

For research based at Toronto Academic Health Science Network (TAHSN) hospitals, students need to obtain Research Ethics Board (REB) approval from the hospital first, and then submit the REB approval letter, approved application form, Research protocol, and appendices for administrative review by the University of Toronto REB. Administrative reviews are normally approved within two weeks. Once received, students should submit a copy of the REB approval letter to the Graduate Assistant to put in the student’s file.

Applications for approval can only be submitted after the proposal has been approved. Students must be listed as a researcher or investigator with the relevant Research Ethics Boards. While the University of Toronto sometimes exempts student research from full ethics review, students must apply for such exemptions and supply the appropriate documentation to the IHPME graduate office. Students must never assume that their research is exempt from ethics approval. Students who do not have documented University of Toronto ethics approval will not be allowed to proceed to their defence.

IHPME students are required to take the online tutorial TCPS 2: CORE (Course on Research Ethics), an introduction to the 2nd edition of the Tri-Council Policy Statement: Ethical Conduct for Research Involving Humans (TCPS 2). Upon completion, you will be able to print or email a Certificate of Completion to be submitted to the IHPME graduate office.

UofT REB Application

The Office of Research Ethics at the University of Toronto has launched an online application process. Here is the landing page to submit an application: My Research 

Please consult the Research Involving Human Subjects resource and Federal Guidelines (TCPS2)

For more information on Research Ethics, or if you have questions about submission, please contact: or 416 946 3273.

Research and Writing

Once the research proposal is approved and ethics approval is obtained the student may begin working on their doctoral research including participants’ recruitment, data collection, data analysis and writing. Some parts of the research such as scoping or systematic reviews may begin before REB approval is obtained. However, it is not advisable to begin before the proposal is approved because the proposal examination committee may have some comments and suggestions to improve the study.

Research and writing are conducted under the guidance of the supervisor in consultation with the thesis research committee. The committee should meet as a whole at least twice a year and submit a meeting report to the graduate assistant after each meeting.

Writing support:

Many students find writing to be one of the hardest parts of PhD. The Writing Centre, the Graduate Centre for Academic Communication (GCAC) and the Health Sciences Writing Centre both offer support for graduate students including one-on-one consultations. 

Financial Support for Research and Publication

Ideally, your supervisor will have some grants to cover some research-related expenses you may incur, such as compensation to study participants, transcription of interviews, travel for  data collection, presentation at conferences, or publication in open access journals 

  • IHPME offers a small grant (currently $500) to support students.
  • Many conferences offer travel fellowships for students to present their work. 
  • SGS also offers a research travel grant and a conference grant for students.
  • The University of Toronto has signed agreements with a number of publishers to support open access publication of research.

Final Oral Exam (FOE)

When the supervisor and thesis committee agree that the thesis is complete and ready for defence, they may proceed with setting up the final oral exam (FOE). The process of setting up the FOE takes approximately two months as outlined below; thus, you will need to plan ahead. 

Please consider the SGS deadlines and recommended dates and timeline below:

Deadline Request for Defence (recommended dates)Last Scheduled Defence (recommended dates)Deadline for Submission of Completed Thesis to SGSExpected Convocation
PhD: June 24, 2024
MSc: July 8, 2024
August 19, 2024PhD: September 16, 2024
MSc: September 30, 2024
PhD: October 16, 2024
MSc: October 30, 2024
mid-December 2024PhD: January 15, 2025
MSc: January 24, 2025
March (in absentia*) or June
PhD: January 20, 2025
MSc: February 3, 2025
March 17, 2025PhD & MSc: April 11, 2025June
*in absentia (no ceremony)

Student or supervisor must submit the completed booking request form and full CVs of all proposed external appraiser and external and internal examiners to the graduate assistant (the external appraiser is often the same person as the external examiner). 

Graduate assistant contact:



The external and internal examiners will then be approved by the IHPME Graduate Coordinator and then by the School of Graduate Studies. This may take up to two weeks.

  • The student submits the thesis to the graduate assistant to send out to the external and internal examiners. The graduate assistant will send the thesis and letters to the examiners.    
  • The student is responsible to send the thesis to their committee. 

A written appraisal from the external examiner should be received 2 weeks before the FOE. The supervisor and student should discuss the written appraisal and how to respond to the comments during the FOE.

SGS will secure a chair for the FOE. The graduate assistant will notify the student, committee and examiners of the appointment of the chair and the time and location of the defence.

The student should arrive 15-30 minutes early to meet with the graduate assistant and set up the room.. 

The Examination Committee

SGS provides comprehensive guidelines for the FOE and the composition of the exam committee.  

The initial process for the FOE is to select an external appraiser and the members of the FOE committee.

The FOE committee includes at least four but no more than six voting members. IHPME strongly encourages selecting a date and time that accommodates the entire FOE committee.

The FOE committee includes:

  • Up to three members of the student’s supervisory committee may vote at the examination. Additional members of the supervisory committee may sit on the FOE as non-voting members.
  • An external examiner.  SGS distinguishes between external appraiser, who reviews the written thesis and provides a written assessment, and external examiner who is part of the examination committee. While SGS allows different people to serve as external appraiser and external examiner, IHPME strongly prefers that the external appraiser also serves as the external examiner (who is a voting member of the FOE committee).
  • An internal examiner
  • Optional: a departmental representative (usually the emphasis lead, program director, or graduate coordinator) who is a voting member of the FOE committee.

Examiners and Appraisers:

It is the responsibility of the supervisor and student to nominate a suitable External Examiner/Appraiser. The supervisor recommends the External Examiner to the Program Director and the Graduate Coordinator for approval. 

  • An appointment with a graduate department (for examiners at the University of Toronto, this is the School of Graduate Studies).
    Note: Internal examiners may be granted a temporary appointment for the purpose of the thesis examination if sufficient advance request (greater than 2 months) is made to the Program Director (who in turn makes the request to the IHPME appointments committee).
  • Recognized expertise in the field being examined.

  • Must be external to the University of Toronto as well as to its affiliated teaching hospitals and their research institutes. 
  • Must be a recognized expert on the subject of the thesis, and an Associate or Full Professor at their home institution, and experienced as a successful supervisor of doctoral candidates through to defence. An appraiser from outside the academic sector must possess the qualifications to be appointed to an academic position at this level. 
  • Must be at arm’s length from both the Candidate and the supervisor(s). Normally, this will exclude anyone who:
    • has served as Masters or PhD Supervisor / Supervisee of the Candidate or the Supervisor;
    • has, in the past six years, been a departmental colleague (e.g. in the same research institute or hospital division) of the Candidate or the Supervisor, or has collaborated on a research project, grant, scholarly work or publication, with either of them.

Note: The Vice Dean (Students), in considering nominations of external appraisers, will assess whether the nominee is at arm’s length. 

According to SGS, the FOE committee must include “at least two examiners who have not been closely involved in the supervision of the thesis. Those eligible include the External Appraiser, members of the faculty appointed to the Candidate’s graduate unit, and members of the faculty appointed to other graduate units of the University.”

However, in IHPME we apply stricter rules:   

The External Examiner:  

  • Although the external appraiser need only fulfill the role of Appraiser i.e., provide a written assessment of the thesis, and need not ultimately vote, IHPME strongly encourages Appraisers to act as External Examiner and to vote at the examination committee. The External Examiner can participate in person or by teleconference/ online.
  • If the external appraiser is unable to serve as an examiner, we expect the external examiner to meet the same criteria as the external appraiser in terms of their academic rank and conflict of interest

Similarly, IHPME applies stricter criteria for the Internal Examiner in that:

  • The PhD internal examiner should have an associate professor rank or higher
  • The PhD internal examiner may be internal to the University of Toronto. Preference is for an examiner who is external to IHPME, however, this is not a strict requirement and those who are internal to the department of IHPME are eligible
  • The PhD internal examiner must have an arm’s-length relationship with the student and supervisor as defined by the same criteria as the external appraiser.
  • In rare cases, when it is proven difficult to find an internal examiner who meets the above criteria, the Graduate Coordinator may approve an internal examiner who meets the SGS criteria but not the stricter IHPME ones.

What to Expect at the Defence

  • A quorum of the Defence Committee must be present.
  • The Chair appointed by SGS follows clearly established examination procedures.
  • The student is asked to leave the room.
  • The defence Committee discusses the internal and external reviews.
  • The student is recalled and presents their thesis (maximum 20 minutes, uninterrupted).
  • One or two rounds of questions are posed to the student. (*Note: Questions can be asked about both the oral presentation and written thesis.)
  • Student is asked to leave the room.
  • The defence Committee votes on the acceptability of both the thesis and the oral defence.
  • The Supervisor informs the student if modifications are required.

After the Defence

  1. After the defence, the Chair of the defence sends the signed and completed ballot to the SGS examinations office.  There are two possible decisions:
    • Adjourn: if there is more than one negative vote and/or abstention, the examination is adjourned and a reconvened examination must be held within one year
    • Pass: There are three options the thesis may be accepted “in present form”, with “editorial corrections” (one month to make changes with supervisor approval), or requiring “minor revisions” (three months to make changes with sub-committee approval).   See SGS Guidelines for the Doctoral Final Oral Examination (FOE) for more detailed information for each case.

After modifications and approval, the supervisor or subcommittee convenor informs SGS that the student has made the corrections, and the student uploads the thesis to ProQuest.  

As of September 1, 2009, the School of Graduate Studies will ONLY accept the submission of theses in electronic format. Please view SGS – Producing your Thesis webpage for information on electronically submitting your thesis.

  1. Students failing to complete all steps by the SGS deadlines will be required to register and pay fees for another term.
  2. The School of Graduate Studies notifies students about convocation arrangements 4–6 weeks in advance.

Finance Your Degree

At IHPME, we offer a variety of financial supports to help you succeed in our graduate programs.

Learn More About this Program

HSR Program Director

Katie N. Dainty
Email Address: katie.dainty@​

Co-leads the management of the HSR Program.

Graduate Administrator

Zoe Downie-Ross
Phone Number: (416) 946-3486
Email Address: ihpme.grad.admin@​

Coordinates student records, graduate funding, and student-related awards.

Graduate Admissions

Christina Lopez
Email Address: ihpme.admissions@​

Manages admissions and responds to all related inquiries.

Graduate Assistant

Nadia Ismail
Phone Number: (416) 946-4100
Email Address: ihpme.grad.assist@​

Coordinates various graduate initiatives including defences, student events, and graduation.

HSR Program Assistant

Anita Morehouse
Phone Number: 416-946-3922
Email Address:​

Manages the HSR courses including enrolment, grades, and access to Quercus.