Japan has abundant hot springs resources that have been empirically used for medical treatment and recreation for people with various diseases or injuries. In 1926, the University of Tokyo inaugurated the Department of Physical Medicine for the scientific study of the effects of hot springs on the human body and mind. Thereafter, balneological research institutes or spa hospitals were established that were affiliated with six national universities; Kyushu, Hokkaido, Okayama, Tohoku, Kagoshima and Gunma had been established by 1951. Although these balneological institutes, including the University of Tokyo, greatly advanced the basic and clinical research on the therapeutic effects of hot springs, they all were either closed or integrated into the main hospital of the university between 1994 and 2018, owing both to government reforms to national universities and decreased government financial support. A brief history of each institute and several titles of published research studies performed there are provided in this article.   The closing of these research institutes is regrettable; however, balneological research is today an important field that contributes to maintenance and promotion of health for the sharply rising number of aged people in Japan. It is expected that a member of the Japanese Society of Balneology, Climatology and Physical Medicine will further develop balneological research using advanced scientific technologies, based on the results achieved in the seven historical institutes mentioned above.