Microsporidiosis is considered to be emerging opportunistic infection in immunocompromised individuals worldwide. The aim of this study was to identify the specific serum antibodies to intestinal microsporidia Encephalitozoon cuniculi and Encephalitozoon intestinalis in women with Human Papillomavirus HPV and without HPV by the indirect immunofluorescence (IFA). From total number of 669 examined women, 225 were HPV positive and 444 women HPV negative. Overall the study comprised of 10.8% women with positive result for presence of E. cuniculi antibodies. In group 1 (HPV-positive women) it was more than 28% and in group 2 (HPV-negative women) it was less than 2% (p<0.001). E. intestinalis infection was found in total of 4.48% women, in group 1 it was present in less than 6% and in group 2 in less than 4% of women.