BackgroundResearch shows that medical education is characterized by unequal conditions for women and men, but there is a lack of qualitative studies investigating the social processes that enable and maintain gender inequalities that include both male and female students. In this focus group study, we therefore explored male as well as female medical students’ experiences of the gender climate – i.e., how beliefs, values, and norms about gender were communicated – during clinical training and how the students dealt with these experiences.MethodsFocus group interviews were conducted with 24 medical students (nine men) at Umeå University, Sweden. The interviews were structured around personal experiences in clinical training where the participants perceived that gender had mattered. Data were analysed using qualitative content analysis.ResultsThe students described gender-stereotyped expectations, discriminatory treatment, compliments, comments, and demeaning jargon. Female students gave more personal and varied examples than the men. The students’ ways of handling their experiences were marked by efforts to fit in, for example, by adapting their appearance and partaking in the prevailing jargon. They felt dependent on supervisors and staff, and due to fear of repercussions they kept silent and avoided unpleasant situations and people rather than challenging humiliating jargon or supervisors who were behaving badly.ConclusionsEveryday communication of gender beliefs combined with students’ adaptation to stereotyped expectations and discrimination came across as fundamental features through which unequal conditions for male and female students are reproduced and maintained in the clinic. Because they are in a dependent position, it is often difficult for students to challenge problematic gender attitudes. The main responsibility for improvements, therefore, lies with medical school leadership who need to provide students and supervisors with knowledge about gendered processes, discrimination, and sexism and to organize reflection groups about the gender climate in order to improve students’ opportunities to discuss their experiences, and hopefully find ways to protest and actively demand change.Electronic supplementary materialThe online version of this article (doi:10.1186/s12909-016-0803-1) contains supplementary material, which is available to authorized users.