The diagnosis of intestinal microsporidiosis has traditionally relied on light microscopy. Western literature shows PCR to be more sensitive and specific. The present study was conducted to assess the prevalence of enteric microsporidiosis in HIV seropositive patients using PCR. Five percent stool samples were found to be positive for microsporidia by pan microsporidia primers and found to be Enterocytozoon bieneusi on amplification using species specific primers. Microsporidia is grossly under-reported in our country and there is a dire need to institute measures to detect this organism particularly in HIV infected individuals to abate morbidity and mortality due to this organism.