Six primers based to sequence of the small sub-unit (ssu-rRNA), conserved sequences of the ribosomal RNA internal transcribed spacer region (ITS) and large sub-unit ribosomal RNA (lsu-rRNA) for the PCR have been used for species-specific detection of microsporidian spores of the genus Encephalitozoon: E cuniculi, E hellem, E intestinalis in the stool.