The main purpose of the study was to examine whether health professions students in Taiwan who study in different programmes experience similar patient autonomy-related professionalism dilemmas caused by disconnections between school and clinical culture. To investigate this issue, we draw specifically on situated learning theory and its cultural concept to examine their professionalism dilemma narratives that were collected through interviews. Of the 79 interviewed students, nearly half of them experienced patient autonomy dilemmas caused by conflicts between school and clinical culture, which have significant negative impacts on their learning and emotional wellbeing. Four major types of patient autonomy-related dilemmas emerge from the data. It was also found that when school culture and clinical culture clash, the latter has a greater influence on students. Thus, the study argues that Taiwanese students' frequent encounters with patient-autonomy dilemmas highlight the challenges faced by health professions students in transferring knowledge between school and clinical cultures, and clinical culture has a more powerful influence on their behaviour and clinical decision making. This phenomenon should be taken into account when organizing health professions education.