JC virus (JCV) causes a fatal demyelinating disease in AIDS patients known as progressive multifocal leukoencephalopathy (PML), and there is evidence that JCV establishes latency in the kidney in a significant part of the human population. This investigation was undertaken to study the latency of JCV in human central nervous system (CNS) and the possible role of the virus in multiple sclerosis (MS). Using oligonucleotide primers specific for the coding region genes (early and late), JCV DNA was amplified from brain tissues by the polymerase chain reaction (PCR). The results indicated that neither normal nor MS brain tissues contained detectable levels of JCV DNA. There are two possible explanations for these negative results. Either the virus is focally distributed and the sections which were tested in this study lacked the viral DNA, or the amount of viral DNA in the tissues was lower than the detection limit of our PCR assays. In addition an intron~ differential RNA PCR was developed to detect large T~antigen and small t~antigen mRNAs in the presence of the genomic DNA which usually contaminates mRNA preparations. Using primers spanning introns, large T and small t mRNAs were detected in brain tissues from PML patients with and without AIDS and in JCV~induced hamster brain tumors. This method may find application in identifying active viral oncogenes in tumor tissue, and in distinguishing active from inactive JCV infections of the brain.