Seven AIDS patients with central nervous system (CNS) disease and cytomegalovirus (CMV) DNA in cerebrospinal fluid (CSF) were evaluated before and 3 weeks after standard ganciclovir treatment by nested polymerase chain reaction (PCR) on limiting dilutions and by quantitative PCR. After therapy, PCR CSF was negative for CMV in 3 patients with low baseline levels of CMV DNA and positive with decreased DNA titers in 4 patients with higher baseline levels. CMV pp65 antigen in polymorphonuclear leukocytes was found in 6 of 7 patients before therapy and in none of 5 after therapy. At autopsy, CMV was found in the CNS of the 4 cases examined, including 3 whose CSF was continuously positive by PCR. Quantitative PCR of CSF is useful for monitoring ganciclovir treatment in CMV infection of the CNS. In AIDS patients, standard ganciclovir treatment seems effective in reducing but not suppressing viral replication in severe cases of CMV infection of the CNS.