The emergence of HIV-resistant strains generally occurs during treatment failure. A high rate of viral replication, low patient adherence to therapy, poor drug absorption or increased drug metabolism may be related to treatment failure and favour the onset of resistance. Recently, despite the absence of detectable HIV viral load in plasma, the importance of the persistence of HIV replication in other reservoirs has been underlined. Paired semen and plasma specimens stored from HIV male patients were tested using the LiPA assay, detecting genotype mutations related to Nucleoside Reverse Transciptase Inhibitors (NRTI) resistance. Overall, 32 paired semen and plasma samples were analyzed. The presence of HIVsequences was determined in 13 paired specimens (40.6%). Sixteen semen and 10 plasma specimens failed to amplify. At least one mutation was identified in the plasma of 77.8% of treated and 50.0% of naive patients. Similarly, mutations were identified in the semen of 66.7% of treated and 50.0% of untreated patients. Different mutation patterns between the two compartments were found in 46.2% of patients. The use of rapid assessment of HIV resistance in plasma and semen may be useful in some situations, such as HIV infection transmitted by sexual contact. Our data reinforce the evidence that, regarding HIV replication, the male genital tract must be considered as a separate compartment from the plasma.