IMIM was created by the City Council of Barcelona in 1947, following the suggestion of the then Director of the Hamburg Tropeninstitut, Professor Nauck, to Dr. Trias de Bes, who was the Director of the then Hospital of Infectious Diseases which is today's Hospital del Mar. Thanks to the support of Dr. García Tornel, who then was the Health Assistant to the Mayor, IMIM's creation became a reality.
The Research Institute, under the management of doctors Jordi Gras and Amadeo Foz is consolidated as research Centre and teaching in the 60's-70's decade, being specially relevant the study of cholera onset in 1971 carried out by Dr. Foz.
At the end of 1984, the creation of IMAS as an autonomous organization in charge of Health Care at the County level, unfolded a specific research policy in County Hospitals, and the establishment of a specific budget.
In 1991 IMIM received the Board of Universities' accreditation as a University Institute, and in 1992 the Antidoping Laboratory of IMIM was responsible for the antidoping control tests for the Olympic and Paralimpic Games taking place in Barcelona.
IMIM is one of the main institutions driving the creation and start up of the Biomedical Research Parc of Barcelona (PRBB), a scientific and innovative project aiming at ranking Barcelona as one of the main biomedical research capitals in Europe. To make the project possible an agreement was signed on April 11 of 2000 between the Barcelona City Council, the Departments of Universites, Research and Information Society (DURSI) and the Department of Health and Social Security of the Generalitat of Catalonia, the Universitat Pompeu Fabra and IMAS.
IMIM is located at the new Barcelona Biomedical Research Park (PRBB) facilities since October 2006.
On 16 December 2013, the Accreditation Committee of the Carlos III Health Institute (ISCIII) approved the acreditation of IMIM as a Health Research Institute, which was ratified by the State Secretarial of Research, Development and Innovation for the Order of 17 February 2014.