The relationship between clinician teachers and their students is of major importance in medical education. However, there is little known about the effects on clinicians when conflict occurs with their students. What do clinicians perceive to be major causes of these conflicts? How do they react when and after conflict occurs? A phenomenological inquiry exploring the lived experience of 12 clinician teachers in medical schools was performed. The clinicians were selected using purposeful sampling and snowballing techniques. The interviews revolved around discussions based on episodes of conflict with medical students that the clinicians considered significant. The analysis and emergent themes were partially constructed around and informed by theories of conflict, and conflict management. A number of themes emerged from this study. Clinicians experienced that significant psychological and behavioural problems of students had a dominant impact on the likelihood and severity of conflict; these conflicts had a significant emotional impact on clinicians; though the responses to conflict varied, "avoidance" was a mechanism commonly used by clinicians and thus the assessment of attitudinal and behavioural professional issues in the workplace was problematic. This study shows how the clinician perspective to challenging student/clinician encounters impacts on the quality of education they are able to provide. We recommend medical schools consider these issues when designing their programs in order to develop and maintain clinician-teacher engagement and participation.