Encephalitozoon intestinalis infection of sows is reported from a pig farm in Slovakia. Spores were detected by direct microscopic visualisation in the faeces of 25 out of 27 sows (92.6%). This finding was also supported serologically by the presence of specific anti-E.intestinalis antibodies and by a species-specific polymerase chain reaction (PCR). This is the first report on E. intestinalis infection of swine in Europe.