BACKGROUND: Coinfection with HIV-1 and HTLV-1 diminishes the value of the CD4 + T-cell count in diagnosing AIDS, and increases the rate of HTLV-1-associated myelopathy. It remains elusive how HIV-1/HTLV-1 coinfection is related to such clinical characteristics. Here, we investigated the mutual effect of HIV-1/HTLV-1 coinfection on their integration sites (ISs) and the clonal expansion. METHODS: We extracted DNA from longitudinal peripheral blood samples from 7 HIV-1/HTLV-1 coinfected individuals, and from 12 HIV-1 and 13 HTLV-1 mono-infected individuals. The proviral loads (PVL) were quantified using real-time PCR. Viral ISs and clonality were quantified by ligation-mediated PCR followed by high-throughput sequencing. RESULTS: The PVL of both HIV-1 and HTLV-1 in coinfected individuals was significantly higher than that of the respective virus in mono-infected individuals. The degree of oligoclonality of both HIV-1- and HTLV-1-infected cells in co-infected individuals was also greater than that in mono-infected subjects. The ISs of HIV-1 in cases of coinfection were more frequently located in intergenic regions and transcriptionally silent regions, compared with HIV-1 mono-infected individuals. CONCLUSION: HIV-1/HTLV-1 coinfection makes an impact on the distribution of viral ISs and the clonality of virus-infected cells and thus may alter the risks of both HTLV-1- and HIV-1-associated disease.