A medical image classification system includes an acceptance apparatus, a medical image acquisition apparatus, and a medical image classification apparatus. The acceptance apparatus includes an acceptor that accepts the input of patient identification information and medium identification information, and a first storage that stores first association information. The medical image acquisition apparatus includes an identification information acquirer, an image acquirer that acquires a medical image for diagnosing a patient, and a second storage that stores second association information. The medical image classification apparatus includes a first acquirer that acquires the first association information stored by the first storage, a second acquirer that acquires the second association information stored by the second storage, and a classifier that performs classification of the medical image identification information per the patient identification information based on the medium identification information in the first association information and the second association information.