A research survey was conducted to find out which diagnostic classification systems were commonly used in university hospitals in Japan. By using a questionnaire, we collected data to determine which diagnostic classification systems and diagnostic criteria were being used to identify schizophrenia, affective (mood) disorders, and neurosis. The results indicated that most university hospitals used either the International Classification of Diseases (ICD) of the WHO or the Diagnostic and Statistical Manual of Mental Disorders (DSM) of the American Psychiatric Association. For research of academic presentations, more than 60% of the surveyed institutions used DSM. In clinical settings, however, ICD and DSM were used with similar frequencies (42–43%). It was also noted that 15% of institutions still use a traditional psychiatric diagnosis for schizophrenia and mood disorders. This paper addresses historical aspects of the diagnosis and classification of mental illness in Japan.