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To evaluate the frequency of drug-resistant HIV-1 viral strains from patients presenting with primary infection in 1999–2000 and to survey the molecular epidemiology of these viruses circulating in France.Resistance mutations were detected by sequencing the reverse transcriptase and the protease genes in plasma samples from 249 individuals. Phylogenetic analysis was performed on the reverse transcriptase genes.Ten per cent of patients [26/249; 95% confidence interval (CI) 7–15%] presented with virus mutations associated with resistance to at least one antiretroviral drug. The distribution of the resistance mutations was as follows: to nucleoside reverse transcriptase inhibitors in 19 (8%; 95% CI 5–12%) and to non-nucleoside reverse transcriptase inhibitors in 10 (4%; 95% CI 2–7%). Primary resistance mutations to protease inhibitors were detected in 14 (6%; 95% CI 3–9%). Twelve patients (5%; 95% CI 3–8%) presented with virus harbouring mutations associated with resistance to two or three classes of antiretroviral drugs. The median HIV RNA in plasma at enrolment was lower in patients with one or more drug resistance mutations than in patients with no mutations (5.05 log versus 5.47 log, P = 0.05). Phylogenetic analysis revealed that 19% (14–24%) of patients harboured HIV-1 non-B subtype strains; this proportion remained high when Caucasian patients only were considered (14%).This study, performed within the French network on HIV-1 primary infection survey, revealed no change in the frequency of resistant viral strains over time, but showed an increasing prevalence of non-B subtypes overall and among Caucasian individuals.