Enterocytozoon bieneusi is a microsporidian parasite found only in the enterocytes of the small bowel of HIV positive patients, producing chronic diarrhea and malabsorption. Since January 1990, we have seen the 13 first Mediterranean cases, diagnosed on duodenal pinch biopsy samples. Diarrhea was the major symptom in all instances, and E. bieneusi was the sole identified pathogen in 6 cases. The diagnosis was made on HES or Giemsa-stained paraffin sections and on Giemsa-stained smears (9 cases). In 3 cases, the parasite was also found on ileal biopsies, but was never encountered in the colonic mucosa. In all patients, transmission electron microscopy of the duodenal mucosa was used, and it confirmed the diagnosis of intestinal microsporidiosis. No instance with negative optic examination had evidence of an infection by E. bieneusi with electron microscopy. Due to the small size of the spores, routine fecal parasitological diagnosis is still a difficult procedure, but it is possible that greater experience may avoid many of today's invasive investigations. Cytologic and histologic routine examination of paraffin sections of the distal duodenal or ileal mucosae is a reliable method to diagnose intestinal microsporidiosis in HIV-positive patients with diarrhea.