Physician autonomy is currently threatened by the external application of pay for performance standards and required conformity to practice guidelines. This phenomenon is being driven by concerns over the economic viability of increasing per capita health care expenditures without a concomitant rise in favorable health outcomes and by the unjustified marked variations among physicians' practice patterns. Proponents contend that altering the reimbursement system to encourage physicians to make choices based upon the best available evidence would be one way to ensure better outcomes per health care dollar spent. Although physician autonomy is most easily justified when decisions are made by appealing to the best available evidence, incentivizing decision-making risks sacrificing physician autonomy to political and social forces if the limitations of evidence-based medicine are not respected. Any reimbursement system designed to encourage physicians to utilize the best available evidence by providing financial incentives must recognize physicians who try to play to the numbers as well as physicians who refuse to follow the best available evidence if doing so would conflict with good medicine or patient preferences. By designing, promulgating, and updating evidence-based clinical practice guidelines, medical specialty societies can limit threats to physician autonomy while improving medical practice.