Clinical reasoning has been defined as a form of cognition applied to evaluating and managing a patient's medical problem. As a kind of cognition, a product of the human psyche, it is logical to expect that clinical reasoning should be best understood through methods derived from psychology, neuropsychology and the cognitive sciences. However, the application of scientific methods to evaluating clinical reasoning is unable to analyse clinical reasoning in terms of first-person experience and consciousness. By reducing clinical reasoning to its cognitive components the cognitivist approach tends to ignore the larger context in which clinical reasoning occurs. By reducing its conception of clinical reasoning to its cognitive components, the neuropsychological approach fails to acknowledge clinical reasoning as a form of intentionality, a gestalt, grounded in human perception. A full epistemology of clinical reasoning requires a phenomenological analysis that can make sense of the relation between pre-reflective consciousness and explicit forms of knowing. In this paper I conciliate cognition and consciousness in medicine through analysing the phenomenology of perception in clinical reasoning. I compare the application of phenomenology to clinical reasoning with the attempt to model clinical reasoning on Aristotelian practical wisdom or phronesis. Finally, I analyse empathy as a type of perception critical for effective clinical interaction and exemplary for reflecting on perception as the intersubjective foundation of clinical reasoning.