OBJECTIVE: To evaluate nested PCR for Toxoplasma gondii (TOX), JC virus (JCV) and Epstein-Barr virus (EBV) for diagnosis of toxoplasmic encephalitis (TE), progressive multifocal leukencephalopathy (PML) and primary central nervous system lymphoma (PCL). METHODS: A prospective study encompassed 26 HIV-1-infected individuals presenting with focal neurologic signs and symptoms. Nested PCR was performed on both supernatants and pellets of centrifuged cerebrospinal fluid (CSF), on plasma and on white blood cells (WBCs). For a retrospective study, stored CSF supernatants were available from an additional 27 HIV-1-infected patients with TE, PML, and PCL. RESULTS: TE, PML or PCL was diagnosed in 13 of 26 patients in the prospective group. Plasma and WBC analysis by PCR was not informative except in one case of TE. TOX and JCV were detected by PCR in the CSF pellets of four of five patients with TE, and of four of five patients with PML, respectively, but in no other cases. EBV was detected not only in three of three cases of PCL, but also in six patients suffering from other conditions. PCR on the CSF supernatants was less sensitive for all three etiologies. These results correlated with those of the retrospective PCR analysis, for which only stored CSF supernatants were available, revealing sensitivities of 33%, 50% and 66% for TE, PML and PCL, respectively, but specificities of 100%. CONCLUSIONS: In the clinical routine, TOX and JCV PCR on centrifuged CSF pellets can be recommended to obtain an early diagnosis of TE and PML. Under these conditions, EBV PCR helps to exclude PCL as a cause of FBLs, as it is highly sensitive, but not specific, for PCL in HIV-1-infected individuals.