BACKGROUND: In developing countries, Isospora belli and Cyclospora cayetanensis frequently cause chronic diarrhea in HIV-infected patients. OBJECTIVE: To compare 1 week of trimethoprim-sulfamethoxazole treatment and 1 week of ciprofloxacin treatment in HIV-infected patients with chronic diarrhea caused by I. belli and C. cayetanensis. DESIGN: Randomized, controlled trial. SETTING: HIV clinic in Port-au-Prince, Haiti. PATIENTS: 42 HIV-infected patients with chronic diarrhea due to I. belli (n = 22) or C cayetanensis (n = 20). INTERVENTIONS: Patients were randomly assigned to receive oral trimethoprim-sulfamethoxazole (160 mg or 800 mg) or ciprofloxacin (500 mg) twice daily for 7 days. Patients who responded clinically and microbiologically received prophylaxis for 10 weeks (1 tablet orally, three times per week). MEASUREMENTS: Treatment success was measured by cessation of diarrhea and negative stool examination at day 7. Prophylaxis success was measured by recurrent disease rate. RESULTS: Diarrhea ceased in all 19 patients treated with trimethoprim-sulfamethoxazole. Eighteen of 19 patients had negative results on stool examination at day 7 (95%). Among the 23 patients who received ciprofloxacin, diarrhea ceased in 20 (87% [CI; 66% to 97%]) and 16 had negative results on stool examination at day 7 (70%). By survival analysis, diarrhea from isosporiasis and cyclosporiasis ceased more rapidly with trimethoprim-sulfamethoxazole than with ciprofloxacin. All patients receiving secondary prophylaxis with trimethoprim-sulfamethoxazole remained disease-free, and 15 of 16 patients receiving secondary prophylaxis with ciprofloxacin remained disease-free. CONCLUSIONS: A 1-week course of trimethoprim-sulfamethoxazole is effective in HIV-infected patients with cyclosporiasis or isosporiasis. Although ciprofloxacin is not as effective, it is acceptable for patients who cannot tolerate trimethoprim-sulfamethoxazole.