Since ancient times epidemics have been a central topic in Chinese medical thought. The explanations for their emergence, spread and transmission, however, have ranged widely. Whereas much of the populace believed in transmission by demons, elitist medical theory, since at least the second century, has emphasized cosmological and meteorological factors. This paper introduces the different approaches to epidemics in general, examining the etymological, historical and medical literature of early Imperial times. It then traces two lines of tradition in Chinese medical thought: one supporting contagionism, the other opposing it. The controversy that began as early as the fourth century, peaked in the twelfth century and ended only with the modern era, reveals a widening gap in the elitist medical theory--the dichotomy of empirical knowledge and theoretical framework.