The aims of this paper are to identify the issues and forces that were the impetus for two recent developments in academic medicine, evidence-based medicine (EBM) and medical decision making (MDM); to make explicit their underlying similarities and differences; and to relate them to the fates of these innovations. Both developments respond to concerns about practice variation; the rapid growth of medical technology, leading to a proliferation of diagnostic and treatment options; the patient empowerment movement; and psychological research that raised questions about the quality of human judgment and decision making. Their commonalities include: use of Bayesian principles in diagnostic reasoning, and the common structure embedded in an answerable clinical question and a decision tree. Major differences include: emphasis on knowledge or judgment as the fundamental problem; the status of formal models and utility assessment; and the spirit and tone of the innovation. These differences have led to broader acceptance of EBM within academic medicine, while decision analysis, the fundamental tool of MDM, has been less welcomed in clinical circles and has found its place in guideline development, cost-effectiveness analysis, and health policy.