Transmission of human and murine cytomegalovirus (CMV) with transfusions and organ transplantation suggests that the latent virus is located in multiple organs and perhaps multiple cell types. The direct identification and localization of the latent virus in the normal host has been difficult using standard culture and hybridization techniques. In vitro amplification using the polymerase chain reaction followed by oligonucleotide hybridization can be used to detect murine CMV DNA. When this method was applied to DNA extracted from latently infected mice, it allowed detection of viral nucleic acid not detected by standard Southern hybridization. The results of these studies support the presence of latent murine CMV in multiple organs including the salivary gland, spleen, and kidney. Amplification and detection of viral DNA in purified renal tubule preparations suggest that this may be a site of viral latency and potential source of the virus during renal transplantation.