Groundstones of microbiology at Charles University Faculty of Medicine in Prague were given by professor Jaroslav Hlava, an outstanding pathologist, who worked also in the fields of bacteriology and serology and infectious diseases. He forced his younger fellow Ivan Honl to organize bacteriology as an independent subject. Together they published first monograph on Bacteriology (1890). Ivan Honl was the world first who performed a real antibiotic therapy using pyocyanase in 1898. He also implemented modified rabies vaccination (Prague technique), studied pathogenesis of meningitis and plaque and iniciated the use of BCG vaccine to prevent tuberculosis. He transformed former bacteriology department to the Institute of Bacteriology and Serology, which became a center where a lot of future czech and slovak top experts e.g. Vojtech Mucha, Dionýz Blaškovič, Josef Ungar, Ivan Málek, Vladimír Wagner started their professional carrier. After Honl´s death in 1936, a new head of the institute professor František Patočka continued further development of the disciplines . Even after closing czech universities by german nazis in 1939 activities of the team continued inside the Bacteriology diagnostic department  situated in the building of Hlava´s department of pathology. After the world war II, in 1945, František Patočka freshly inspired by his clerkship in the United States, organized in the building of former german university institute across the street a contemporary conception of the Institute of  Microbiology and Immunology. In his article on the history of czechoslovak microbiology published in 1983, Patočka characterises his contributon using followin words: „Majority of my work had grown from diagnostics. I tried to transfer to our science all that seemed to me to briefly described or unclear. I studied bacterial antagonism, anaerobes, rickettsiae, viruses, especially influenzaviruses and porkpoliomyelitis ones. Studies in Corynebacteria, Listeriae and Mycoplasmas were derived exclusively from diagnostic practice.“ Leading scientific program of the institute was focused on pathogenesis, immunogenesis, diagnostics and epidemiology of anthropozoonoses .  Patočka´s students and coworkers enriched the program with other topics such as influenza, TBE, enterotoxigenic E. coli, automation of bacterial diagnostics, bacterial  resistance to antibiotics, biology of anaerobes (Clostrididium sordellii), factors of pathogenicity of haemolytic Corynebacteriae (world priority description of D-sphingomyelinase) . Since 1955, scientific output had been supported by a newly organised department – Laboratory for special medical bacteriology and immunology 

After Patočka´s retirement in 1969, the new head, Assoc. professor Ctirad John turned the scientific profile of both the Institute and the Laboratory more to immunology and  following topics were studied: principles of adjuvantimmunisation and immunomodulation, topographic overview of  antibody creation by cellular methods, listeria factor Ei as immunomodulator, the role of lipids in immunisation activities of the czech BCG vaccine, immunomodulation activity of Propionibacteriun parvum a Bacillus firmus,spontaneous and directed chemotaxis of phagocytes, mucosal immunity. Immunology was lectured by prof John within medical microbiology, clinical immunology was taught in internal medicine.. In 1991 a special obligatory course of  medical immunology  was implemented in the curricula.

In1994, based on the fusion of Laboratory for specialised microbiology an immunology with the department of Clinical immunology of the 1st Clinic of Internal Medicine (dept organised by prof. Strejček in 1972), indepenent Institute of Clinical Immunology was found., headed by prof. Terezie Fučíková DSc. Besides education and scientific activitiesthe institute provided outpatients´s diagnostic and therapeutical care and superconsulting service not only for departments of the General Faculty Hospital, but for doctors from the whole republic.

In 2001 the Institute for Medical Microbiology and the Instititute for Clinical Immunology fused again. The new head, prof. Ivan Šterzl organized a modern centre for research, education, diagnostics and medical care with new approaches to laboratory service from clinician´s side. New research teams were formed focused on autoimmunity, immunoendocrinology, prionic diseases and pathogenesis of Helicobacter pylori.