Hepatitis B virus is one of the most common infectious disease in the world, infecting two billion people, 350 million of them being chronically infected. It is primarily transmitted through contact with body fluids of the infected person. The aim of the study was to determine prevalence and factors associated with hepatitis B virus infection among patients attending Special Treatment Centre clinic in Nairobi. The blood samples were taken for serological analysis of hepatitis B proteins. The samples were transported to KEMRI where they were screened for Hepatitis B surface antigen (HBsAg), hepatitis B antibodies and antibody to the HBV core protein (HBcAb) using commercially available kits. A total of 200 adults; 80 males and 120 females aged 18- 60 years with a mean age of 32.77, SD=8.638 and a median of 31 years participated in the study. In general, 9.5% (95% CI 7.3–12.4) of the respondents were positive for hepatitis B surface antigen while 26.5% (23.4-29.5) respondents were positive for Hepatitis B surface antibody. The prevalence of HBsAg among males and females was 10% (8/80) and 9.2% (11/120) respectively. A multivariate analysis of risk factors showed that multiple sex partners (p=0.001), presence of genital ulcers (p=0.001) and not using condom (p=0.0013) were associated with HBV infection. None of the study participant reported having been vaccinated against hepatitis B virus. Data on sociodemographic characteristics, information on sexual behavior, and clinical characteristics were collected using a semi structured interviewer administered questionnaire. This current study has revealed that HBV infection is also endemic among patients attending special treatment Centre. Therefore, this study group constitute a target population for further HBV prevention and treatment through provision of condom, early treatment of genital ulcer, health education on consistent condom utilization and need for having one sex partner. Routine immunization with hepatitis B (HB) vaccine is strongly recommended for the prevention of HBV infection in individuals at risk for STIs.