Knowledge of the genetic diversity of HIV-1 constitutes a fundamental premise in the epidemiological surveillance. In the present study, the HIV-1 genetic variability from 142 Cuban patients who were diagnosed with HIV-1 infection during 2009 and 2010 was determined. HIV-1 subtypes were determined by partial RT-PCR and sequencing of the HIV-1 pol gene. The phylogenetic analysis showed that 47 (33.1 %) samples were subtypes B and 95 (66.9 %) were non-B subtypes, where G, H, and C subtypes, as well as the recombinant forms CRF19_cpx, CRF18_cpx, and CRFs BG, were included. The circulation of CRF05_DF was detected for the first time in Cuba. The analyses of recombinants showed the presence of recombinant CRF18_cpx/CRF19_cpx. The study confirms the high genetic diversity of HIV-1 and the circulation of new genetic variants in the studied population, which indicates the importance of maintaining constant epidemiological surveillance in Cuba.