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Human herpesvirus 6 (HHV-6) can integrate its genome into the telomeres of host chromosomes and is present in the germline of about 1 % of the human population. HHV-6 encodes a putative integrase U94 that possesses all molecular functions required for recombination like DNA-binding, ATPase, helicase and nuclease activity and was hypothesized by many researchers to facilitate integration, ever since the discovery of HHV-6 integration. However, analysis of U94 in the virus context was hampered by the lack of reverse-genetic systems and efficient integration assays. Here, we addressed the role of U94 and the cellular recombinase Rad51 in HHV-6 integration. Surprisingly, we could demonstrate that HHV-6 efficiently integrated in the absence of U94 using a new quantitative integration assay. Additional inhibition of the cellular recombinase Rad51 only had a minor impact on virus integration. Our results shed light on this complex integration mechanism that includes factors beyond U94 and Rad51.