In order to evaluate the capacity of routine histological examination to detect microsporidiosis, a retrospective study was performed on 72 duodenal biopsies from 72 HIV-infected patients with upper abdominal symptoms of unknown cause. Two light microscopic cytological staining techniques, modified trichrome stain and the fluorochrome Calcofluor, were used. Two cases of microsporidiosis were detected among the 20 patients with prolonged diarrhoea of unknown origin in whom no etiological agent had been demonstrated by stool examination, mycobacterial and cytomegalovirus culture of biopsies, and histological routine staining of duodenal biopsies. The calculated confidence interval of 3-30% corresponds to the prevalence of intestinal microsporidiosis in HIV patients with prolonged diarrhoea in various parts of the world. The findings motivate attempts to identify microsporidia using special cytological staining methods. Improved methods of species identification are needed to aid in the choice of chemotherapy.