Background: Development of resistance to antiretroviral medication can occur in persons on antiretroviral therapy, acquisition of already resistant strain in persons who have never taken medication or by natural polymorphism of the virus in vivo. This leads to treatment failure hence complicating management of HIV patients. Objectives: To determined the extent of HIV-1 drug resistance mutations in HIV-1 positive drug naïve persons in Kenyan population. Methods: HIV-1 positive plasma samples from seventy-eight (78) drug naïve subjects were collected from Health Centers in five provinces in Kenya. HIV-1 viral RNA was extracted using Qiagen® RNA isolation kit and a 697bp size portion of HIV-1 reverse transcriptase (RT) gene amplified by nested PCR using specific primers and amplified products analyzed by gel electrophoresis and visualized under UV light. The successfully amplified products were directly sequenced using the Big Dye® sequence terminator technology (Applied Biosystems®).Generated sequences were then compared with reference HIVdrug resistance database (http://hivdb.stanford.edu/).