The stormy process of the emergence of new knowledge and their theoretical understanding, the implementation of attempts to automate the processes of diagnosis and treatment necessitate the achievement of rigor and unambiguity of concepts, especially basic ones, such as the concept of «disease». The authors of the article attempted to define the concept of «disease» from the point of view of physiology, using an essential approach that reflects the object (disease) in its content and, most importantly, in development, and not only in manifestations. In the process of formulating a new definition, the existing methodology for establishing a diagnosis was revised and the structure of the medical history was improved, as well as the approach to the treatment of the disease was rethought.