A Comparison of Atovaquone and Pentamidine in the Prevention of Pneumocystis Carinii Pneumonia in HIV-Infected Patients Who Cannot Take TMP/SMX

Inclusion Criteria Concurrent Medication: Allowed: * Antimicrobial agents not specifically prohibited. Concurrent Treatment: Allowed: * Transfusion. Patients must have: * HIV positivity. * Prior PCP (histologically confirmed) OR documented CD4 count \< 200 cells/mm3 OR constitutional symptoms such as thrush or unexplained fever (\> 100 F) for 2 or more weeks. * No current or suspected active PCP, and no signs of active PCP on chest x-ray. * Prior intolerance to TMP/SMX or other trimethoprim or sulfa-containing regimens. * Life-expectancy of at least 6 months. NOTE: * Pregnant women are eligible at the discretion of the investigator. Exclusion Criteria Co-existing Condition: Patients with the following symptoms or conditions are excluded: * Significant psychosis or emotional disorder that would preclude study compliance. * Severe chronic diarrhea (e.g., \> five stools/day) that may negatively affect absorption of oral medication. * Unable to take oral medication or unable or unwilling to take medication with food. Concurrent Medication: Excluded: * Rifampin. * Other investigational agents except for drugs available through Treatment INDs or expanded access programs. * Medications likely to have anti-pneumocystis effect (e.g., dapsone, trimethoprim, pyrimethamine, trimetrexate, other DHFR inhibitors, sulfadiazine, sulfamethoxazole, other sulfonamides, primaquine, clindamycin, and sulfonylureas. * Corticosteroids in greater than physiologic replacement doses for more than 21 consecutive days. * Systemic therapy for CNS toxoplasmosis, Kaposi's sarcoma, lymphoma, other active malignancies, or other disease that may decrease life expectancy or confound assessment. Patients with the following prior conditions are excluded: * History of severe or intractable intolerance to atovaquone or aerosolized pentamidine. * Prior hypoglycemia, pancreatitis, arrhythmias, or severe hypotension associated with any form of pentamidine. * Prior enrollment in this protocol. Active substance abuse that would preclude study compliance.