This study explores the views of doctoral students and supervisors about two doctoral thesis-writing models: the traditional monograph and the thesis that includes published articles in its body. Doctoral theses in biological and health sciences usually follow one of these two common models. Doctoral theses with publications are increasingly utilised in Australian and New Zealand universities. This article provides insights into the factors that doctoral students and supervisors in Australia and New Zealand consider when deciding how to format a student’s thesis. A cross-sectional survey was conducted of supervisors and doctoral students in biological and health sciences at The University of Auckland (UoA) and The Australian National University (ANU). Basic descriptive quantitative data analysis was undertaken. Qualitative data from open-ended survey questions were analysed using a general purpose thematic approach. Overall, 144 completed surveys were returned with a total response rate of 22.9%. More than half of the respondents identified as doctoral students (UoA 54.4%, ANU 73.3%). Respondents’ primary consideration when weighing up the risks and benefits of each thesis model was the impact of publications on furthering aims of both the student and the supervisor. Other points included quality and style of writing, extent of peer review, development of skills, and time management. If they were to embark on another doctorate, most respondents indicated that they would do a doctorate that included published articles in its body. Based on findings, we recommend supervisors of students who are including articles in their thesis should be clear with students from the outset about what their own contributions will be in the writing process, as well as their expectations concerning publication processes and outputs. We argue for a move towards multimodal theses formats.