Microsporidia are obligate intracellular parasites that are recognized as important opportunistic pathogens of immunocompromised and transplanted patients. Enterocytozoon bieneusi and, less frequently, Encephalitozoon intestinalis are the most prevalent species in humans; both of them are associated with enteric infections. Cell cultures have been useful in the study of microsporidia biology. In Colombia, however, no isolates of microsporidia from patients with AIDS have been obtained.A cell culture of intestinal microsporidia was established from stools of positive patients in order to isolate a native strain.Stool from a single AIDS patient was concentrated with the water-ether technique, and the sediment was treated with a mixture of antibiotics and antifungal agents for 18 hours at 37 degrees C. Vero cells were cultivated in 24-well plates with Gibco RPMI medium supplemented with 10% bovine fetal serum and antibiotics. The culture was subsequently inoculated with previously concentrated spores. The medium was changed every second day and the presence of spores was evaluated with the Quick Hot Gram chromotrope stain.Two weeks post-infection, microsporidial spores were identified with characteristic morphology and staining properties. PCR results showed that Encephalitozoon intestinalis was the isolated species.A cell culture of microsporidia was established from a stool sample. This protocol is important to isolate and maintain additional native Colombian strains and it will contribute to biochemical, immunological and epidemiological studies of the currently established strain.