With improving therapeutic protocols, confirmation of microsporidiosis has become increasingly important. We designed a study to determine the best screening method(s) for microsporidian detection in biopsy specimens. Forty-two small intestinal biopsy specimens from 31 immunocompromised patients (68% AIDS) were stained (hematoxylin-eosin [H & E], modified trichrome, Warthin-Starry, and Brown-Brenn) and polarized. Polymerase chain reaction and Southern blot assays were performed on all positive cases. Microsporida were detected in nine cases (21%) by modified trichrome (all patients with AIDS). Of these, seven were Brown-Brenn positive, and five Warthin-Starry positive. Two cases polarized on H & E and three on special stains. Four of nine positive cases were confirmed by molecular studies. We found polarization to be the least sensitive screening method. The modified trichrome was the most sensitive when screening for microsporidiosis in paraffin-embedded biopsy specimens. Furthermore, combining Brown-Brenn or Warthin-Starry with the trichrome stain helps exclude false-positive results due to granular artifacts (eg, eosinophils, Paneth cells).