Disparities in health can result from the clinical encounter between a doctor and a patient. This paper studies three possible mechanisms: prejudice of doctors in the form of being less willing to interact with members of minority groups, clinical uncertainty associated with doctors' differential interpretation of symptoms from minority patients or from doctor's distinct priors across races, and stereotypes doctors hold about health-related behavior of minority patients. Within a unified conceptual framework, we show how all three can lead to disparities in health and health services use. We also show that the effect of social policy depends critically on the underlying cause of disparities.