Genotypic resistance analysis on viral DNA and plasma was performed in 56 therapy naive patients with recent and chronic infection to assess the prevalence of mutations associated with drug resistance and compare cell-free and cell-associated strains. Direct sequencing of DNA provirus disclosed key mutations to RT inhibitors more frequently than in plasma RNA. In addition, major mutations associated with drug resistance in the PR region were only found in PBMCs. Although our data are limited to a small cohort, they show a different resistance profile between plasma and PBMC compartments and may yield additional information for first-line antiretroviral regimens.