Introduction and objectives. Encephalitozoon cuniculi is an obligate intracellular parasite infecting especially domestic rabbits; however, spontaneous infections have been documented in other mammalian species such as dogs, cats, rabbits, horses, cows and sheep all over the world. Encephalitozoonosis is a chronic and latent disease leading to renal failure, encephalitis, disorders of brain and urinary tract, and may lead to death. There are limited reports on encephalitozoonosis in wildlife, which is why the aim of this study was to detect the prevalence of antibodies to E. cuniculi in European hares. Materials and methods. Samples of blood sera from 701 wild hares from the Czech Republic (n = 245), the Slovak Republic (n = 211) and Austria (n = 245) were examined by indirect immunofluorescence antibody test (IFAT); samples with titer ≥ 40 were marked as positive. Results. The total seroprevalence of E. cuniculi antibodies was 1.42% with titres in the range 40-640. Antibodies to E. cuniculi were detected in 2.9% (7/245), 0.8% (2/245) and 0.47% (1/211) hares from the Czech Republic, Austria and the Slovak Republic, respectively. Conclusions. This is the first detection of antibodies to E. cuniculi in hares from Europe showing that hares could be exposed to E. cuniculi infection, however with a low rate.