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Cerebral toxoplasmosis continues to cause high morbidity and mortality in developing countries. The association of sulfadiazine and pyrimethamine is considered the standard therapy; however, it has potential disadvantages. This single-arm open-label clinical trial was carried out in a tertiary hospital in São Paulo, Brazil. We included patients of at least 18 years of age, whose HIV infection was confirmed, and clinical and brain computed tomography (CT) findings were compatible with cerebral toxoplasmosis upon admission. Patients received trimethoprim (TMP) 10 mg/kg/day sulfamethoxazole (SMX) 50 mg/kg/day, in two divided doses. Brain CT was performed at study entry and after two weeks. The endpoints of the study were: (i) the proportion of patients with clinical and radiological response after two weeks of TMP-SMX and (ii) the proportion of patients who discontinued TMP-SMX due to adverse events. Forty-six patients were included (23 males, median age 35 years). The main clinical manifestations were headache, hemiparesis and altered mental status. The proportion of patients who obtained clinical and radiological response after two weeks of anti-toxoplasma treatment was 85% (n = 39). Overall, TMP-SMX was safe, with only 2 (4%) discontinuations due to adverse events. In this study, TMP-SMX was effective and safe in the treatment of HIV-related cerebral toxoplasmosis.