To determine the HIV-1 genetic diversity in Kazakhstan, 85 blood samples from HIV-seropositive donors were collected between 2001 and 2003. The study population consisted of 91.8% injecting drug users (IDUs); the remainder was infected sexually or iatrogenically. A genomic region that included part of the polymerase gene was sequenced for all 85 samples, and from these, 6 samples were randomly selected for nearly full genome sequencing. Subtype A was the most common genetic form (94.1%), followed by CRF02_AG (4.7%) and subtype C (1.2%). All subtype A sequences clustered closely with samples from countries of the former Soviet Union (FSU). From these sequences, 47 (58.8%) presented the secondary protease inhibitor mutation V77I that has been linked to a genetic lineage in the FSU epidemic. In addition, most had the other 2 mutations that characterize the "V77I haplotype." All 6 nearly full-length sequences were subtype A and clustered with other FSU strains. The CRF02_AG strains from this population clustered with strains from Uzbekistan, reflecting the spread of the CRF02_AG epidemic in Central Asia. The HIV epidemic in Kazakhstan is predominantly in IDUs and is indigenous to the geographic region, and most of the strains are genetically similar to those circulating in the FSU and other parts of Central Asia.