Objective: To report the clinical response to atovaquone in HIV-1-infected patients with symptomatic intestinal microsporidiosis. Design: A retrospective review of a cohort of AIDS patients with symptomatic intestinal microsporidiosis who received atovaquone. Setting: Infectious Disease Program of the Grady Memorial Hospital, Veterans Affairs Medical Center and private physicians' offices in Atlanta, Georgia. Patients and methods: HIV-1-infected patients (n = 371) were offered a complete stool evaluation and monthly follow-up. Among them, 22 were diagnosed with intestinal microsporidial infection using stool smears stained with modified trichrome stain. Species confirmation was made by light microscopy or electron microscopy on small intestinal biopsy specimens in some patients. Main outcome measure: Differences in symptoms, number of stools, and body weight were compared before and after a minimum of 1 month of atovaquone therapy. Results: Eight patients received atovaquone treatment. The mean onset of clinical improvement after beginning treatment was 13 days (SEM, ± 2). The mean number of stools per day decreased from 10 ± 2.5 to 2 ± 1 (P = 0.02, paired t test). The mean weight gain was 3 ± 2 kg. The parasite was continuously present in the repeated stool specimens. However, semiquantitative analysis performed on two patients' stool specimens showed a decreased parasite burden. Four patients underwent small intestinal endoscopy with control after a 1-month period. The morphology of the spores by light microscopy was consistent with Enterocytozoon bieneusi in all four patients. Only one out of these four patients demonstrated a decrease in parasite burden in the biopsy specimen. Ultrastructural analysis performed in another of these four patients following treatment demonstrated the presence of electron-dense granules in spores, suggestive of toxic effects. Conclusion: Atovaquone demonstrates promise as a symptomatic treatment for intestinal microsporidiosis. A double-blind and placebo-controlled clinical trial is currently in progress.