A total of 47 avian faecal samples of wild waterfowl (great cormorant - Phalacrocorax carbo, great crested grebe - Podiceps cristatus, white stork - Ciconia ciconia) trapped in the eastern Slovakia were screened for the presence of human pathogenic microsporidia by microscopy and real-time SYBR Green PCR method using species primers and sequenced. Microscopic analysis showed presence in 32 samples (29 cormorants, 3 dippers). Microsporidial DNA (Encephalitozoon cuniculi genotype I) was identified in 19 faeces samples (40.4%) namely cormorants in 17 out of 40, one dipper of 5 and a stork out of 2. The present work describes three new host species of the bird population in microsporidium Encephalitozoon cuniculi genotype I which confirms the theory of low specificity of this species.