A number of published studies suggest that HIV infection accelerates epigenetic ageing. The main aim of this study was to ascertain if HIV infection is an independent factor leading to DNA hypomethylation and accelerating epigenetic ageing in men successfully treated with integrase inhibitor (INSTI)-based combined antiretroviral therapy (cART). Forty-eight (48) men living with HIV receiving INSTI-based cART and fifty (50) uninfected men in the control group were included. All participants filled out a questionnaire probing into lifestyle factors. Global and site-specific DNA methylation and expression of methyltransferase genes were examined in all participants. As well, all patients underwent basic laboratory blood tests. The results were analysed using statistical and machine learning methods. We found a strong association between HIV infection and global DNA hypomethylation as well as significant association with higher expression of the methyltransferase gene DNMT1. However, there was no association with DNA methylation levels of CNOT2, DPP6, FOXG1 and NPTX2 genes or expression levels of DNMT3a and DNMT3b. The results confirm that in men successfully treated with INSTI-based cART, HIV infection is an independent factor causing global DNA hypomethylation and increased DNMT1 expression and thus accelerating epigenetic ageing.