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Background  Investment in research is high on the agenda of many countries in recognition of the fact that research is important for the development of society. Doctoral students have a vital role and represent a substantial part of this investment. It is therefore imperative to reduce the risk of students dropping out from doctoral studies. The aim of this qualitative study was to gain deeper insight into the working conditions of, and obstacles and opportunities for, doctoral students at an institute of medicine in Sweden.    Methods  Semi-structured interviews were conducted in 2013 with 17 doctoral students—of varying genders, professions and fields of research—from the Institute of Medicine, Sahlgrenska Academy, at the University of Gothenburg, Sweden. The recorded interviews were transcribed and analysed using systematic text condensation.    Results  Four categories emerged from the data. They were: Safety, Frustrating Structures, Others - not me, and the future. They included positive as well as negative perceptions. Among the positive perceptions were recognition of the importance of the supervisor, as well as secure conditions, and personal development. Frustrating structures in the academic culture, stress and differences in career building constituted the negative points.    Conclusions  Our findings suggest that there is a need for structures within the university that support doctoral students who feel they are not receiving the assistance they need, who believe they have unreasonable working conditions, or who may need to change supervisors in order to complete their graduate research studies. Our study also highlights the fact that supervisors have a major influence on the work environment of doctoral students, and that the general and academic perception of the research area likewise has an effect on the successful completion of the research project and dissertation. Providing leadership training for supervisors could be an important measure that may help improve conditions for the doctoral students they supervise.    Electronic supplementary material  The online version of this article (10.1186/s12909-019-1684-x) contains supplementary material, which is available to authorized users.

Doctoral students’ perceived working environment, obstacles and opportunities at a Swedish medical faculty: a qualitative study