Following authorization from the Prime Minister, MCRF was reincorporated as a public interest foundation on April 1, 2011.

MCRF was established in December 1958, with funds raised from patent fees of the new antibiotic kanamycin, which was discovered by the late Dr. Hamao Umezawa, then Director of the Department of Antibiotics at the National Institute of Health and Professor of the Research Institute of Applied Microbiology at the University of Tokyo. MCRF’s inaugural President was Shinji Yoshino, while Dr. Umezawa served as the Chairman of the Board. The objectives of MCRF are to conduct microbial and microbiological research to discover beneficial substances and develop and utilize these substances particularly to advance disease prevention and treatment, thereby contributing to an improvement in public health and welfare.

In 1962, MCRF established its Research Institute, Institute of Microbial Chemistry, at its present location and commenced research activities under the directorship of Dr. Umezawa. The institute has since given rise to numerous beneficial pharmaceuticals, including kasugamycin, which is highly effective against rice blast, and bleomycin, which is the first target-specific anticancer antibiotic. Furthermore, the institute initiated research, ahead of the rest of the world, into the mechanism of resistance in strains resistant to aminoglycoside antibiotics such as streptomycin and kanamycin. This research initiative resulted in the successful synthesis of debekacin and arbekacin, derivatives of kanamycin, which are effective against several strains of bacteria.　This background has led to microbiology, medicine, and organic synthetic chemistry becoming the main pillars of the institute’s research activities.

In August 1982, MCRF revised its articles of association, adding “contribution to academic research” to its objectives, on the basis that it had already made significant contributions in that area. Indeed, MCRF has nurtured many researchers, not only for its own Institute but also for universities and businesses.

On the occasion of the renewal of its executive department in 2010, MCRF adopted a policy of further strengthening its basic research. Regarding administration of the institute, a two-director system has been adopted, with each director leading either biological or chemical research and supervising the promotion of science and technology as well as human resource development. In this new system, MCRF will conduct biological and chemical research and development projects under the close collaboration of the two directors; these projects will be based on themes such as the prevention and treatment of diseases afflicting human beings and other living organisms, the maintenance and security of food resources, and the improvement of the global environment.