Objectives Health care students face many situations during their education that might be emotionally challenging. Students are confronted with illness, suffering, death, patient treatment dilemmas, and witnessing unprofessional behaviour on the part of health care professionals. Few studies have focused on what these experiences lead to in relation to the process of becoming a professional. The purpose of the study was to explore medical students main concerns relating to emotionally challenging situations during their medical education. Methods A constructivist grounded theory approach was used to explore and analyse medical students experiences. Data were gathered by means of focus group interviews, including two interviews in the middle and two interviews at the end of the students undergraduate programme. A total of 14 medical students participated. Results Students main concerns relating to emotionally challenging situations were feelings of uncertainty. These feelings of uncertainty concerned: (i) insufficient knowledge and skills; (ii) the struggle to manage emotions in patient encounters; (iii) perceived negative culture and values amongst health care professionals and in the health care system, and (iv) lacking a self-evident position on the health care team. The first two aspects relate to uncertainties concerning their own capabilities and the other two aspects relate to uncertainties regarding the detached medical culture and the unclear expectations of them as students in the health care team. Conclusions In the process of becoming a physician, students develop their professional identity in constant negotiation with their own perceptions, values and norms and what they experience in the local clinical context in which they participate during workplace education. The two dimensions that students have to resolve during this process concern the questions: Do I have what it takes? Do I want to belong to this medical culture? Until these struggles are resolved, students are likely to experience worry about their future professional role.