Provided are a medical image diagnosis system, a medical image diagnosis method, and a program which reduce a burden on a doctor in a case of performing image diagnosis on a large number of medical images, such as a health checkup. The problem is solved by a medical image diagnosis system including at least one processor, and at least one memory that stores a command to be executed by the at least one processor, in which the at least one processor performs first determination of determining whether or not a medical image obtained by imaging a subject is normal, and performs second determination of determining presence or absence of an abnormality from the medical image in a case in which it is determined that the medical image is not normal in the first determination.