Object Toxoplasmic encephalitis (TE), primary central nervous system lymphoma (PCNSL) and progressive multifocal leukoencephalopathy (PML) are major central nervous system (CNS) diseases in patients with acquired immunodeficiency syndrome (AIDS). Weassessed the diagnostic value of polymerase chain reaction (PCR) in the detection of DNAsof Toxoplasma gondii {T. gondii), Epstein-Barr virus (EBV) and JC virus (JCV) in the cerebrospinal fluid (CSF). Methods Wecompared the PCRresults with those of pathological findings at autopsy. Patients or Materials The present study included 23 autopsies representing those in whomCSF samples were obtained before death while the patient was hospitalized or at autopsy. Results The threshold levels for PCR detection were 4 tachyzoites of T. gondii, 5-15 genomes of EBVand 10 genomes of JCV. Weidentified T. gondii DNAin 4 out of5 autopsy-defined cases ofTE, EBVDNAin 5 out of5 cases with PCNSL, and JCV DNAin 2 out of2 cases with PML.The specificity ofPCR was 100% in TE, 78%in PCNSL, and 100% in PML. Conclusion Although the number of cases was relatively small in this study, PCRcorrectly identified T. gondii DNAin those cases in which PMLor PCNSL was the sole clinical diagnosis. Our results indicate that PCRexamination of CSFis a clinically useful tool for the diagnosis of focal brain lesions in patients with AIDS. (Internal Medicine 38: 556-562, 1999)