Peer Physical Examination (PPE) is an educational tool used globally for learning early clinical skills and anatomy. In quantitative research, there are differences in students’ preferences and actual participation in PPE by gender. This novel study qualitatively explores the effect that gender has on medical students’ experiences of learning physical examination through PPE. We employ an interpretative approach to uncover the PPE experiences of students from a European, graduate-entry medical school. Volunteers participated in either individual or group interviews. The data were transcribed, de-identified and analysed using thematic analysis. There was evidence of gender inequity in PPE, with students describing significant imbalances in participation. Male students adopted roles that generated significant personal discomfort and led to fewer experiences as examiners. Assumptions were made by tutors and students about gender roles: male students’ ready acceptance of exposure to be examined and female students’ need to be protected from particular examinations. In contrast with the first assumption, male students did feel coerced or obliged to be examined. Students described their experiences of taking action to break down the gender barrier. Importantly, students reported that tutors played a role in perpetuating inequities. These findings, whilst relating to one university, have implications for all settings where PPE is used. Educators should be vigilant about gender issues and the effect that they may have on students’ participation in PPE to ensure that students are not disadvantaged in their learning.