Human herpesvirus 6 (HHV-6) is the only human herpesvirus encoding U94/rep, homologue to the parvovirus non-structural gene rep68/78. Results to date suggest that HHV-6 U94/rep might regulate viral gene expression and have a role in viral latency. To determine the effect of U94/REP upon viral replication, the protein was produced. The purified U94/REP retained the characteristic immunological features. It was internalized and localized in the nucleus of human cells, showing marked inhibitory activity on the replication of HHV-6 (both variants A and B). The effect of U94/REP was dose-dependent and sensitive to treatment with single-stranded but not double-stranded DNA. U94/REP inhibited the replication of other betaherpesviruses, HHV-7 and human cytomegalovirus, but had no effect on herpes simplex virus. These results confirm the action of U94/rep latency gene in the regulation of HHV-6 replication with implications for co-reactivations and latency of human betaherpesviruses.