Polymerase chain reaction (PCR) was used for the detection of microsporidian DNA in duodenal biopsies obtained from 28 human immunodeficiency virus (HIV)-infected patients with intestinal microsporidiosis. Duodenal biopsies from 23 HIV-infected patients without microsporidiosis served as controls. A generic primer set for human microsporidia was used at first for the PCR. Amplified products were detected in 26 (93%) of 28 biopsies from patients with intestinal microsporidiosis. All control biopsies were negative. Microsporidia species were identified using Southern blot hybridization with specific probes for Enterocytozoon bieneusi and Encephalitozoon intestinalis. This technique confirmed the transmission electron microscopy-based species identification. Similar results were obtained using PCR with species-specific primer sets for E. bieneusi and E. intestinalis. PCR testing of intestinal biopsy specimens can be used successfully for rapid detection and species differentiation of intestinal microsporidia and thus could be a valuable alternative to transmission electron microscopy.