The fermentation theory of disease is the (now obsolete) concept that many diseases, including the diseases which were "epidemic, endemic and contagious," were regarded as owing their origin to the presence of a "morbific principle" in the system, acting in a manner analogous to, although not identical with, the process of fermentation.

It was rendered obsolete by the germ theory of disease, which led to the new science of bacteriology.

See also: Zymotic diseases (for the Greek language term zumoun for "ferment")