Rationale and aim The rapidly changing knowledge base of clinical practice highlights the need to keep abreast of knowledge changes that are most relevant for the practitioner. We aimed to develop a model for reflection on clinical practice that identified the key elements of medical knowledge needed for good medical practice. Method The dual theory of cognition, an integration of intuitive and analytic processes, provided the framework for the study. The design looked at the congruence between the clinical thinking process and the dual theory. A one-year study was conducted in general practice clinics in Oxfordshire, UK. Thirty-five general practitioners participated in 20-minute interviews to discuss how they worked through recently seen clinical cases. Over a one-year period 72 cases were recorded from 35 interviews. These were categorized according to emerging themes, which were manually coded and substantiated with verbatim quotations. Results There was a close fit between the dual theory and participants' clinical thinking processes. This included instant problem framing, consistent with automatic intuitive thinking, focusing on the risk and urgency of the case. Salient features accounting for these choices were recognizable. There was a second reflective phase, leading to the review of initial judgements. Conclusions The proposed model highlights the critical steps in decision making. This allows regular recalibration of knowledge that is most critical at each of these steps. In line with good practice, the model also links the crucial knowledge used in decision making, to value judgments made in relation to the patient.