The latent viral genome, harbored indefinitely, threatens reactivation from its remote location. Although polymerase chain reaction (PCR) has detected the organs responsible for latency, it is not known whether latent cytomegalovirus (CMV) infection is maintained within organ-specific cells or ubiquitous elements such as macrophages, endothelial cells, or perhaps others. PCR lacks correlation with tissue structure. However, PCR-based in situ hybridization maintains cellular architecture while allowing the identification of the latently infected cells. Murine CMV (MCMV) nucleic acid sequences in organs of latently infected Balb/C mice were amplified by PCR incorporating digoxigenin-11-dUTP, holding the product DNA in situ (appropriate controls analyzed in parallel). Product DNA was then hybridized in situ with a biotinylated oligonucleotide probe for detection via streptavidin-alkaline phosphatase and light microscopy. Immunohistochemistry verified the positive cell types. Using this technique, we have shown directly in multiple organs of latently infected Balb/C mice including kidney (5/5), liver (5/5), and spleen (5/5) that the endothelial cell and/or T-lymphocyte harbor latent MCMV, whereas in uninfected animals, MCMV DNA was not detected. PCR-based in situ hybridization allows detection of the specific cell(s) harboring latent MCMV DNA while allowing conservation of cellular architecture.