Cytomegalovirus (CMV) establishes a latent infection in its host; however, the organ sites of viral latency and its mechanism still remain to be fully clarified. To elucidate this issue, a latent infection with murine (M) CMV was attempted to induce in mice and the organ sites of the latent viral genome were examined for more than one year by a polymerase chain reaction (PCR). As a result, latent MCMV DNA was detectable in both the lung and the spleen as late as 59 weeks after infection. The heart was also observed to be a target organ of latent MCMV DNA, though the amount of viral DNA was much less than that seen in the lung and spleen. In germfree (GF) mice, on the other hand, no such latent viral DNA was observed in the spleens, while it was seen, but to a significantly smaller degree, in the lungs and the hearts than in the same organs of specific pathogen-free (SPF) mice. The amount of infectious virions generated in the host appeared to be almost equal between the GF and SPF mice. The above findings therefore suggest that the spleen, lung and heart are target organs for MCMV latency and the indigenous bacterial flora, which are not colonizing in GF mice, play an important role in the establishment of such viral latency in SPF mice.