The microsporidian Enterocytozoon bieneusi has been recognized as an important cause of chronic diarrhea in severely immunodeficient adults infected with human immunodeficiency virus (HIV). We report the first case of intestinal E. bieneusi infection in a child. The 9-year-old boy with connatal HIV infection presented with failure to thrive, chronic diarrhea, and intermittent abdominal pain. His CD4 lymphocyte count was 0.05 × 109/L and dropped to 0.01 × 109/L. No HIV-associated opportunistic infection other than oral hairy leukoplakia and oral candidiasis had been found before microsporidia were detected. Treatment of microsporidiosis with albendazole was of no benefit. During follow-up, the boy also developed intestinal cryptosporidiosis. Evaluation of chronic diarrhea in severely immunodeficient HIV-infected children should include examination for intestinal microsporidia. We recommend the use of a new coprodiagnostic technique that allows detection of microsporidial spores in stool specimens. Furthermore, consideration of dual or even multiple parasitic infections in the differential diagnosis of chronic diarrhea may have both important clinical and epidemiological implication