The history of medicine has brought many theories to explain disease. Hippocrates was the first to say diseases had a cause and diseases were not sent from God. Then came the punitive theory, that diseases were a punishment for behavior. Then came the miasma theory, that diseases came from the air and environment. Then came the theory of spontaneous generation. Then came the germ theory. Then came the theories of inflammation, abnormal proteins, and genetic abnormalities. All of these theories were partially correct, but not the entire explanation. We offer an organizing principle for chronic diseases that supports and goes beyond the prior theories, to explain the root causes of chronic disease.