An infection with Septata intestinalis was diagnosed in a 35-year-old AIDS patient without diarrhoea. The diagnosis was based on morphological examinations of a duodenal biopsy specimen. Serum antibodies were detected reacting with spores of Encephalitozoon cuniculi. Spores of S. intestinalis and E. cuniculi stained with Brown Hopps Gram stain showed a red colour (Gram negative) and not a blue/black colour which was described for microsporidian spores in tissue.