Sequence analysis plays an important role in the management of patients chronically infected with HIV-1. Knowledge of the viral genotype and drug resistance mutations is crucial for the correct management of these patients. From this point of view, the experience of researchers in the HIV-1 field and the introduction of the HIV-1 genotyping resistance test has been fundamental. Several molecular tools are available to assist the provider in interpreting genotypic test results including phylogenetics. However, it should be remembered that antiretroviral drug designs, resistance studies and interpretation systems have been largely based on HIV-1 subtype B, which has been historically the most prevalent subtype in Western countries. Due to increased migration towards Europe, especially from Africa and South- East Asia, the molecular epidemiology of HIV-1 in Western Europe, including Italy, is changing. HIV-1 non-B subtypes have entered Europe and their prevalence has increased over the last years. In Italy, the estimated percentage of infection with non-B subtypes ranges from 2.4 % to 19.4%. However, the true prevalence of HIV-1 non-B subtypes in this country is still not well known and probably underestimated. This may have important clinical and diagnostic implications. A strict molecular epidemiological survey and a reinforced sequencing strategy are required.