Latent endogenic toxicity is the key cause to many hard-to-treat diseases of internal medicine according to latent toxicity theory, and inner-pestilence pathogenesis is a hypothesis developed from sundry-qi etiology. Both the theories source from the disease cause knowledge of epidemic-febrile-disease science of Traditional Chinese Medicine. Syndrome analyzing and differentiating principle, treating way and formulas as well as medicines involved in latent endogenic toxicity theory may be applied to diseases induced by inner pestilence in order to make the evil side turn to the right. Inner-pestilence theory is helpful to understand latent toxicity theory, to master its differentiation principle for symptom-and-sign analysis, meantime, latent toxicity theory construct a pathway to put inner pestilence theory from hypotheses to clinical practices.