Objective: To characterize antiretroviral drug resistance mutations among drug naïve patients in two referral hospitals in Kenya Background: Acquired immunodeficiency syndrome (AIDS) caused by Human immunodeficiency virus (HIV) was first described in 1982. Since then the virus has spread globally to infect millions of people. HIV was first described in Kenya in the period between 1984/1985. Currently, Kenya has an estimated HIV-1 prevalence of 6.2% with a country population of about 40 million people. With the introduction of antiretroviral drugs, the survival of most HIV patients has been prolonged markedly. However this is greatly threatened by increasing rates of antiretroviral dug resistance, which may eventually lead to suboptimal treatment outcomes. Methods: The aim of this study was to determine antiretroviral mutation profiles among drug naïve patients in two referral hospitals in Kenya. Antiretroviral naïve HIV patients in Aga Khan University Hospital and Thika Level 5 Hospital were consecutively recruited to participate in the study. Participants with viral loads >1000 copies/millilitre had their samples screened for antiretroviral resistance mutations by genotypic testing. A total of 121 participants were recruited into this study from two centres. Eighty four participants had their samples successfully genotyped for drug resistance mutations. Results: A total of five NRTI mutations (two Y115F, K219Q, K219E, and T215F) and one V106I mutation against NNRTIs were found among participants in this study. One study participant had one protease mutation, M46L. The estimated primary antiretroviral resistance rate against reverse transcriptase inhibitors was 8.7 % (95% CI 4.0-17.7). Resistance against protease inhibitors was found to be low at 1.46% (95% CI 0.26-7.9). The most common viral subtype was A1 at 52%. Others subtypes included D at 17%, subtype C at 13%, viral recombinants (CRF01_AE, CRF02_AG) at 12%, B at 3% and others subtypes (H, J) at 3%. Conclusion: Antiretroviral drug resistance mutations are showing an increasing trend among therapy naïve patients since the introduction of antiretroviral therapy in Kenya in the early 2000. This might affect the efficacy of antiretroviral regimens used for treating HIV patients. Funding: The study was co-funded by the Aga Khan University Research Council Grant (URC Grant Project 102001KEN Under Dr Nancy Okinda) and Aga Khan University Postgraduate Medical Education Seed Funding.