The current research areas in the Institute of Experimental Medicine are a result of its history. It was officially founded in 1975 by combining four medical research laboratories that had been organized twenty years before. Three of the laboratories had been affiliated with clinical departments of Charles University, i.e., the Department of Plastic Surgery, the Department of Ophthalmology, and the Department of Otorhinolaryngology. The fourth laboratory was closely connected with the Department of Histology of the First Medical Faculty and was oriented toward cell and tissue ultrastructure. Under the leadership of the renowned Professors Burian, Kurz, Přecechtěl and Wolf, the laboratories established themselves in the world of medicine and contributed significantly to the international recognition of Czechoslovak medical research. The four laboratories, although intellectually strong and reasonably well-equipped, suffered from physical isolation and lack of collaboration. Therefore, it was considered to join the laboratories and to establish an Institute of Experimental Medicine under the Czechoslovak Academy of Sciences.
An otolaryngologist, Prof. Vlastimil Kusák, was appointed as the first director (1975–1984). The research spectrum was extended by inviting to the Institute a group of immunologists (Dr. Jiří Franěk, Dr. Karel Nouza), and by establishing a laboratory to investigate the health effects of mycotoxins in Eastern Bohemia (Olešnice, Orlické Mountains).
In the seventies and eighties, the profile of the Institute crystallized, particularly in the period when most of the laboratories were transferred to a building on Legerova street and, subsequently, when Prof. Jiří Elis was appointed director (1984–1990). Research areas broadened to include the electron microscopic investigation of the cell nucleus and nucleolus, particularly in blood cells; the morphological tracing of nucleic acids; the morphology and immunocytochemistry of the thyroid gland and pancreas; mechanisms of local immunity, cancer immunity and graft-versus-host reaction; biochemistry and histochemistry of the eye; corneal pathology and the testing of contact lenses; the morphology of the inner ear and its changes under the influence of noise; the electrophysiology of the central auditory system; the basics of genotoxicity and teratology; the mechanisms of normal and pathological development of orofacial region and teeth, epidemiology of orofacial clefts; and the testing of mycotoxins.
While several groups and individuals succeeded in reaching a high standard of scientific work, the Institute as a whole suffered from scattered topics, a lack of internal communication and many other obstacles characteristic of life in the seventies and eighties.
In the beginning of the nineties, several parallel processes led to the harmonizing of the scientific orientation of the Institute as well as of its human capital. These processes comprised not only the change in the political situation in the country but also a significant rejuvenation of the Institute. In 1990, Prof. Jelínek, Head of the Laboratory of Teratology, was appointed director of the Institute (1990–1994). The structure of the Institute was reorganized on the basis of a free competition of internal projects and further strengthened by its success rate in the competition for grants from the Grant Agency of the Academy of Sciences. The involvement of members of the Institute in both the teaching of medical students and in ecologically oriented research increased, particularly concerning the adverse effects of exogenous factors on the organism.
Important for the formation of the improved profile of the Institute was the entrance of two new strong scientific groups in 1991 – the Laboratory of Cellular Neurophysiology from the Institute of Physiological Regulations, headed by Prof. Eva Syková, and the Laboratory of Genetic Ecotoxicology, headed by Dr. Radim Šrám (a joint laboratory with the Regional Hygiene Station of Central Bohemia). Clinically oriented groups ceased to exist in the Institute or were transferred to clinics. In 1993 the Institute moved to a new building in Prague-Krč, where several other biomedical institutes of the Academy of Sciences are located. In 1994, Prof. Josef Syka was appointed director (1994–2001). In the same year the Institute passed successfully through the evaluation process within the Academy of Sciences. Important changes in the organization of the Institute that have taken place since that time have focused its orientation and improved its scientific profile.
Prof. Eva Syková was appointed as director in 2001 (2001–2016). In 2002 the Institute’s research program further increased through the establishment of new groups, growing to its current size. The reason for this change was the affiliation of the former Institute of Pharmacology ASCR and the Department of Molecular Embryology from the Institute of Animal Physiology and Genetics ASCR.
From 1 January 2007, the Institute was transformed into a public research institution established by the Act No. 341/2005 Coll. , on public research institutions. In 2010 the institute celebrated the 35th anniversary of its founding.
At present, the Institute of Experimental Medicine belongs to the biomedical group of research institutes of the Academy of Sciences of the Czech Republic and is the only institute in the Czech Republic engaged in a comprehensive medical research program encompassing a number of diverse fields.
In 2015, the Institute celebrated the 40th anniversary of its founding.