Kitasato Institute was established in 2008 through the integration of the former Kitasato Institute and Kitasato University. It was originally founded in 1914 by Dr Shibasaburo Kitasato as Japan's first private medical research facility. Together with Germany's Robert Koch Institute and France's Pasteur Institute, The Kitasato Institute has become one of the world's top microbiology institutes. Headquartered in Shirokane, Tokyo where it was founded, the Institute administers Kitasato University as well as two vocational schools and two affiliated institutions. As Japan's only academic organisation to possess facilities for vaccine production, the Institute contributes to the eradication of infectious diseases and the improvement of public health.

While the Institute, integrated with Kitasato University, strives for greater advances in specialized educational and research fields, it also promotes research to apply these results to clinical situations. In addition, it is strengthening integrated efforts in various areas, from basic research and drug discovery to vaccine development (at its infection control research and educational centers), team medicine education, integrated agricultural and medical research, health promotion and environmental preservation. The Institute also devotes itself to clinical trials and research to achieve beneficial integration of high-quality, safe pharmaceutical development through the collaboration and aims of its four hospitals, as well as a beneficial combination of Western and Oriental medicine.