Human immunodeficiency virus (HIV) characterized by a high genetic variability includes two genotypes namely HIV-1 and HIV-2. A major proportion of the infections worldwide is caused by HIV-1 which includes four groups (M, N, O and 13). Group M being responsible for the HIV pandemic is further divided into nine genetically distinct subtypes (A, B, C, D, F, G, H, J, and K). Additionally, more than 49 circulating recombinant forms (CRFs) have been recognized up to now. The aim of this study was to determine the subtype characterization and prevalence of HIV strains isolated from patients inhabiting in Istanbul, Turkey. The study was carried out between June 2009 and June 2012 and a total of 72 patients [58 male, 14 female; age range: 20-57 (median: 37) years; CD4(+) T cell count range: 3-813 (median: 243)/mm(3); HIV-RNA load range: 1.5+E3-1.0+E7 (median: 5.8+E5) IU/ml] were included in the study. Fortysix of the patients (64%) have acquired the infection via heterosexual and 23 (32%) via homosexual contact. Of the patients 57 were newly diagnosed and antiretroviral (ARV) therapy-naive patients, while 15 were under different ARV therapies. For HIV-1 subtyping the most widely known algorithm (HIVdb-Stanford University Genotypic Resistance Interpretation Algoritm) was used. The population-based sequencing of the reverse transcripta ise region (pol) of HIV-1 indicated that CRFs (36/72; 50%) were the most commonly identified strains, followed by subtype B (31/72; 43%) among Turkish patients. Sub-subtypes A1 (3/72; 4.2%) and F1 (2/72; 2.8%) were also detected as low prevalent. The recombinant forms of HIV-1 circulated in Istanbul, Turkey were found as follows, respectively; CRF02_AG [%25 (18/72), West Africa, Central Africa and Middle East/North Africa origin], CRF12_BF [%12.5 (9/72), South America origin], CRF03_AB [%9.7 (7/72), Eastern Europe and Central Asia origin] and CRF01_AE [%2.8 (2/72), South-East Asia, East Asia and Central Africa origin]. Since molecular epidemiologic studies are important tools for tracking the transmission and spread patterns, and for the control of the HIV infections, HIV molecular studies should be expanded in HIV-1 infected Turkish patients. Furthermore, the determined subtypes and CRFs of HIV-1 in Turkey may be expected to contribute to global HIV surveillance systems.