Background Enhanced HIV surveillance using demographic, behavioral, and biologic data from national surveys can provide information to evaluate and respond to HIV epidemics efficiently. Methods From October 2012 to February 2013, we conducted a 2-stage cluster sampling survey of persons aged 18 months to 64 years in 9 geographic regions in Kenya. Participants answered questionnaires and provided blood for HIV testing. We estimated HIV prevalence, HIV incidence, described trends in HIV prevalence over the past 5 years, and identified factors associated with HIV infection. This analysis was restricted to persons aged 15–64 years. Results HIV prevalence was 5.6% [95% confidence interval (CI): 4.9 to 6.3] in 2012, a significant decrease from 2007, when HIV prevalence, excluding the North Eastern region, was 7.2% (95% CI: 6.6 to 7.9). HIV incidence was 0.5% (95% CI: 0.2 to 0.9) in 2012. Among women, factors associated with undiagnosed HIV infection included being aged 35–39 years, divorced or separated, from urban residences and Nyanza region, self-perceiving a moderate risk of HIV infection, condom use with the last partner in the previous 12 months, and reporting 4 or more lifetime number of partners. Among men, widowhood, condom use with the last partner in the previous 12 months, and lack of circumcision were associated with undiagnosed HIV infection. Conclusions HIV prevalence has declined in Kenya since 2007. With improved access to treatment, HIV prevalence has become more challenging to interpret without data on new infections and mortality. Correlates of undiagnosed HIV infection provide important information on where to prioritize prevention interventions to reduce transmission of HIV in the broader population.