Abstract Background Media exposés and academic literature reveal high rates of bullying and harassment of medical students, most commonly by consultant physicians and/or surgeons. Recent reports reveal the medical profession to be characterised by hierarchy, with verbal abuse a ‘rite of passage’, as well as sexist and racist behaviours. Methods Semi-structured in-depth interviews were conducted with ten current or recently graduated medical students from Sydney-based medical schools. Interviews were audio-recorded, transcribed verbatim, and thematically analysed. Results Hierarchy, and a culture of self-sacrifice, resilience and deference, were identified as problematic elements of the medical profession. In the minds of participants, these factors created barriers to reporting mistreatment, as participants felt reporting led to being labelled a ‘troublemaker’, affecting career progression. Additionally, participants stated that avenues of recourse were unclear and did not guarantee confidentiality or desired outcomes. Conclusions Mistreatment is continuing in clinical teaching and has negative consequences on medical students’ mental health and learning. Structural change is needed to combat institutionalised mistreatment to ensure the wellbeing of future doctors and high quality patient care.