The well-being of doctoral students is an important issue. Previous studies examining the well-being of university students have targeted undergraduate populations or international students and used mental health measures. Measures of mental health (e.g. Mental Health Inventory), however, do not capture the personal, emotional and social as well as the cognitive, technical and institutional impacts on research students’ experience. There is also growing realization in the field (White, 2013) that current satisfaction scales used to measure candidate experience in higher education are not taking into account the emotion and well-being of the candidate. Hence the need for measures of well-being that take into account the impact of the experience of doctoral study on the person. In order to support doctoral student well-being, there is a need for the right instruments to measure this. The process of the development of a doctoral well-being questionnaire reported in this paper, used a new approach based on the methodology outlined by Juniper, Walsh, Richardson & Morley (2012) and recent findings about student learning at doctoral level, especially interview data generated in a study of student metacognition (Cantwell, et al., 2015). The purpose of the interviews was to understand those aspects of their research study that were personally important to students and how they approached their learning and dealt with problems and issues. This paper describes the development of a questionnaire based on the major themes that emerged from the interviews with doctoral students and their perceptions and experiences of doctoral study. In particular the study focussed on identifying those aspects of being a researcher that doctoral students identified as having the greatest negative impact on overall well-being. The questionnaire was constructed to assess the range and the relative importance of seven domains: institution, research task, supervision, research self-efficacy, social and personal, work/life balance and future career opportunities that have an impact on their well-being. This approach represents a change in focus from previous questionnaires that examine how the student’s well-being impacts on their research work to how their research work impacts on their well-being. There were significant differences in student well-being by age, first language, gender, level of degree, and full and part time status.