The thesis should consist of Introduction, Methods, Results, and Discussion. Frequent use of headings or subheadings may help to unify the thesis. Numbering the sections "4 deep" (e.g. 1.2.1.b) may be useful. Examine other recent theses as possible models. Follow the Guidelines for Producing Your Thesis. The required PhD Thesis forms are available at http://www.sgs.utoronto.ca/currentstudents/Pages/Thesis-Forms.aspx
For the PhD thesis the Introduction and Discussion must adequately cover the research area directly related to the results and topic of the thesis. As a general guideline, the length of the Introduction should be anywhere from 30-50 pages, with adequate detail, but using concise scientific writing. The length of the discussion will vary depending upon the thesis style, ie. compilation of papers versus the more traditional single discussion. Either way, the discussion should also be kept within a reasonable length, with adequate detail, but using concise scientific writing avoiding repetition (as a guideline, not over 50 pages).
The Introduction should contain an organized review of the literature that introduces the reader to the field and leads naturally to the hypotheses to be tested. Failure to organize the review material around one or more summary Tables or Figures frequently leads to confusion. The Results may consists of a series of chapters which are based on the content of draft or published papers in the usual format (Abstract, Introduction, Methods, Results, Discussion). However, these chapters cannot be the actual papers which will likely be collaborative to a greater or lesser extent and thus may not represent the work of the student. Often, readers find repetition of introductory concepts and methods to be tedious to read and therefore it is better to use a single Results section. The final Discussion should clearly establish the novelty and importance of your contribution to knowledge, should consider alternate interpretations of the data and suggest any necessary qualifications and future lines for experimentation. The References are collected at the end of the thesis in the format which is used for your preferred journal.
Subject to the approval of the Supervisory Committee, you may decide to omit some of your work from the Results and include them instead in an Appendix. It is much easier to write a coherent story if you leave out extraneous experiments that do not contribute to the main thesis or which cannot be readily interpreted or defended.
Remember to make appropriate Acknowledgements, especially if other students have helped in any important way; they may wish to use shared material in their own theses. If you decide to include in your Results work generated by others then you must be prepared to defend all aspects of this work. If you are not prepared to defend them, then just mention these data in the text or leave them for an Appendix.
Any text that is copied or paraphrased from other sources must be between quotation marks and must be referenced. Otherwise this is plagiarism. This is a serious offence at the University of Toronto and can result in dismissal. Please see How Not to Plagiarize. It is almost never appropriate to quote material from the work of others.
Students who want to submit their thesis to committee members by email should consult the committee member prior to sending the document. Although some faculty members will read the thesis on the computer, many prefer to edit a hard copy. If you are thinking of sending faculty a thesis by email, check first to see whether that person wants to read it on a computer. Do not expect that faculty will print your thesis and be sure to send original versions (no photocopies) of the figures. When you distribute a printed thesis make sure that pages are numbered and bound. If the thesis is printed on 3-hole punched paper it is easy to insert in a 3-hole binder.