We report two cases of prolonged fever in deeply immunocompromised patients with AIDS who had been receiving trimethoprim-sulfamethoxazole (TMP-SMZ) as primary prophylaxis for several months. Investigations of the cause of fever yielded normal or negative findings except that the polymerase chain reaction (PCR) for Toxoplasma gondii in the blood was positive in both cases, and PCR of the bronchoalveolar lavage fluid was positive in one case. After a few days of treatment with pyrimethamine plus clindamycin, the two patients became afebrile and the T. gondii PCR became negative. The patients probably had disseminated toxoplasmosis attenuated by TMP-SMZ. PCR examination of blood for evidence of T. gondii genome may be useful in screening for causes of unexplained fever in patients with AIDS, even those who receive prophylaxis with TMP-SMZ.