Gammaherpesviruses (GHVs) are members of an emerging subfamily of the family Herpesviridae. A recent study identified a novel GHV in domestic cats (Felis catus GHV1, FcaGHV1), and epidemiological surveys have found that FcaGHV1 is distributed worldwide. In this study, we investigated the prevalence of GHVs in domestic cats in Japan with a molecular epidemiological survey. Blood samples were collected from 1,738 domestic cats and GHV-derived DNA was detected with PCR in 1.3% (23/1,738) of the Japanese domestic cats. The FcaGHV1 detected in this study was very similar to FcaGHV1 detected in a domestic cat in North America. Older age (>5 years old) and Feline immunodeficiency virus infection were identified as risk factors for GHV infection.