The primary goal of evidence-based medicine (EBM) has been to change the way clinicians make decisions. But EBM has inappropriately privileged the results of clinical research for medical decision making and has undermined the importance of other kinds of medical knowledge, pathophysiologic understanding and clinical experience, to clinical practice. Here, the specific advantages and limitations of each kind of medical knowledge are examined. No particular kind of medical knowledge is necessarily more compelling than the others when it comes to making specific patient care decisions. Several cases where medical knowledge is conflicting are examined to demonstrate the weighting and negotiation necessary for sound clinical judgement. Expert clinicians must utilize a variety of reasons and methods of reasoning in arriving at the best clinical decision or recommendation for an individual patient. The process can be formalized and made explicit, but it cannot be narrowed, simplified and focused only on the results of clinical research.