Medical Education 2012: 46 : 216-227 Context  Clinical reasoning is the cornerstone of medical competence. Difficulties in this area are often identified late in clinical training. Studies point to challenges faced by clinical educators in their dual roles as clinicians and educators. Little is known about the common, yet complex, issue of how they manage clinical reasoning difficulties. We therefore sought to: (i) describe the current state of affairs in various clinical teaching settings, and (ii) explore the factors that determine the behaviour of clinical educators in this respect. Methods  Four focus groups were conducted with 26 clinical educators in general practice, internal medicine and emergency medicine in Belgium and Switzerland. Two researchers analysed the transcripts of the focus group discussions using Fishbein's integrative model of behaviour prediction in a theory-driven, immersion-crystallisation process. Experienced faculty members validated the findings. Results  Across diverse settings, the process of identifying and remediating clinical reasoning difficulties was unstructured. Consistent with Fishbein's model, clinical educators' underlying beliefs determined their behaviour. They believed in the apprenticeship model of learning in the clinical environment, in which their educational role was limited to role-modelling and in which residents were responsible for assimilating skills. They were sceptical about the potential impact of remediation. A few more knowledgeable supervisors had a stronger sense of their educational role, but did not implement systematic procedures to manage clinical reasoning difficulties. Environmental constraints were symptomatic of a collective paradigm of residency as an apprenticeship, in which the focus is on clinical duties, rather than as an educational programme. Conclusions  In order to improve the current state of affairs in the management of clinical reasoning difficulties, a collective paradigm shift is required to alter the perception of residency as an apprenticeship to one of residency as a structured educational programme. Faculty development programmes should be designed in an integrated way so that they not only develop clinical educators' skills, but also modify their beliefs.