Small bowel mucosal fragments from a human immunodeficiency virus-positive female patient with chronic diarrhea were investigated by transmission electron microscopy, and Isospora belli enteritis was documented. The submicroscopic profile was characterized by a moderate abnormality of mucosal architecture with reduction in height of villi and hypertrophy of crypts. Stages of both asexual (trophozoite, schizont and merozoite) and sexual (macrogametocyte) phases of the life cycle of the parasite were identified in the epithelium, always enclosed within a parasitophorous vacuole. Moreover, the presence of occasional extracellular merozoites in the intestinal lumen and in the lamina propria near or within lymphatic vessels was documented. These findings expand the current knowledge of this parasite regarding its capacity to survive in an extracellular environment and document a possible mechanism by which extraintestinal infection can take place.