Research capacity is increasing in low- and middle-income countries (LMICs), with progressive development in the range and complexity of studies being undertaken, often in collaboration with high-income country partners. Although senior local stakeholders are typically involved in ensuring that research is conducted according to accepted standards for ethical and scientific quality, to date there has been little exploration of the views of younger generations around the ethics of research involving human subjects. We present our protocol to establish a longitudinal mixed-methods student cohort at the University of Medicine and Pharmacy at Ho Chi Minh City, Vietnam, that is investigating students’ views around the ethics of clinical and public-health oriented research. We use a synergistic approach involving initial deliberative engagement activities (e.g. science cafes, debates) to inform participants about complex concepts, prior to formal quantitative and qualitative methods (surveys, focus group discussions and in-depth interviews) that are designed to explore the students’ views in detail. We focus in particular on dengue, as an example of a locally relevant disease, and probe students’ thoughts on such themes as appropriate remuneration for research participants, involvement of vulnerable groups, use of human challenge trials in LMICs etc. A snapshot of the cohort and its activities after one year is also presented; among 429 active students, primarily from the Faculty of Medicine, the proportions of male and female students were similar, the majority were from southern or central Vietnam where dengue is endemic, and available data indicates the cohort to be representative of the expected spectrum of socioeconomic groups. The cohort provides a unique resource to investigate the views of young people on medical ethics, an important but hitherto underrepresented group in such discussions. Feedback indicates a clear interest in contributing thoughts and ideas to the development of clinical research in Vietnam.