PhD in the field of medicine is more common than in any other domain. Many medical doctors are driven towards PhD, but also students with other backgrounds (usually MSc) are conducting a PhD in medical schools. Higher education has invested a lot in developing generic and research competences. Still little is known about how PhD students themselves perceive the competence of future PhDs. The aim of this study is to determine how medical PhD students perceive their future competences and whether there is a difference between MD PhD and MSc PhD students' perceptions. Moreover this study examines students' perceptions of their learning environment and their experienced well-being. The data were collected from 163 medical PhD students. The survey data consisted of Likert type statements, open-ended questions and background variables. PhD students' perceptions of acquired competences were content analysed. The connection between conducted degree and emphasised competences were analysed using cross tabulation and ?[superscript 2]-test Perceptions of well-being and the learning environment were examined using descriptive statistics of scales. The results showed that PhD students considered a wide variety of competences to be central to future PhDs. Their perception of their future competences consisted of scientific and generic competences. All students emphasised scientific competences over generic competences but MSc PhD students emphasised generic skills more than MD PhD students. PhD students' perceptions of their well-being and the learning environment showed that PhD studies are a burdening and stressful process. However students also felt that they received feedback from the scientific community.