Faecal samples were collected from 377 horses on 23 farms with varying management systems in the Czech Republic. Microsporidia were found on 16 farms and the overall prevalence of Enterocytozoon bieneusi and Encephalitozoon cuniculi was 17.3% (66/377) and 6.9% (26/377), respectively. The prevalence of E. cuniculi in horses over 3 years of age was significantly higher (10.0%) compared to younger horses (4.0%). No significant differences in prevalence were observed among stallions, geldings, and mares for both microsporidia. Significantly higher infection rates of E. bieneusi and E. cuniculi were recorded in horses kept in stables than those on pasture. Two genotypes of E. cuniculi (I and II) and 15 genotypes of E. bieneusi including six previously described and nine novel genotypes were detected. The most common genotype detected was E. bieneusi genotype D identified in 51.5% (34/66) of positive horses. The identification of E. bieneusi genotypes D, EpbA, G and WL15, which were previously reported in pigs, humans, raccoons and horses, indicates that horses could be a potential source of zoonotic infection in humans.
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