The history of ancient medicine is inseparable from the history of ancient religion, because healing in most ancient cultures was a religious function before it was a naturalistic one, and the separation of the two was never complete even in Greek and Roman contexts where naturalistic medicine was most developed.

The Asclepion — the healing sanctuary dedicated to the god Asclepius — was the primary medical institution in classical Greece and Rome. Patients came to the Asclepion, underwent ritual purification, and slept in the incubation hall (enkoimeterion), where the god would appear in a dream and prescribe treatment. The cures recorded at the great Asclepions at Epidaurus, Pergamon, and Cos ranged from the plausible (diet, rest, bathing) to the miraculous (blindness cured, severed limbs restored).

Hippocratic medicine coexisted with the Asclepia rather than replacing them. The great sanctuary at Cos was associated with the Hippocratic tradition; Galen worked at the Asclepion of Pergamon. The relationship between temple medicine and naturalistic medicine was complementary rather than competitive: the Asclepion provided the religious and social context of healing, while Hippocratic practitioners provided the naturalistic examination and diagnosis.

Egyptian medical papyri (the Edwin Smith Surgical Papyrus is the most famous) show a mixture of empirical observation and magical prescription in proportions that vary by condition. Surgical conditions — wounds, fractures, dislocations — were treated with impressive empirical accuracy; internal conditions were more often referred to magical remedies. This is a rational distribution given the available tools: surgery can be observed and results assessed; internal medicine without diagnostic imaging is much harder to evaluate empirically.