Enteric infection with the protozoan Isospora belli is common in patients with the acquired immunodeficiency syndrome (AIDS) and causes severe diarrhea. I. belli responds well to treatment with trimethoprim-sulfamethoxazole, but there is a high rate of recurrence. To investigate the effect of long-term prophylaxis, we studied 32 Haitian patients with AIDS complicated by I. belli infection and chronic diarrhea. All were treated with trimethoprim (160 mg) and sulfamethoxazole (800 mg), given orally four times a day for 10 days; the patients were then randomly assigned to receive 500 mg of sulfadoxine and 25 mg of pyrimethamine weekly, 160 mg of trimethoprim and 800 mg of sulfamethoxazole three times a week, or placebo. Half of the patients (5 of 10) who received placebo had recurrent, symptomatic isosporiasis a mean of 1.6 months after the initial treatment. All 22 patients who received either trimethoprim-sulfamethoxazole or sulfadoxine-pyrimethamine remained asymptomatic. I. belli was identified in the stools of only one of these patients, who was receiving trimethoprim-sulfamethoxazole. The study medications were generally well tolerated but had to be discontinued in the cases of two patients because of severe pruritus. In 10 patients, the prophylactic regimen has been continued for a mean of 16 months without recurrent isosporiasis. We conclude that isosporiasis in patients with AIDS can be treated effectively with a 10-day course of trimethoprim-sulfamethoxazole and that recurrent disease can subsequently be prevented by ongoing prophylaxis with either trimethoprim-sulfamethoxazole or sulfadoxine-pyrimethamine.