Abstract: Despite risks of HIV transmission to infants born of the HIV positive women, con- traceptive use is uncommon among women in HIV discordant partnerships. The aim of this study was to determine the factors associated with contraceptive use in a clinical trial cohort of HIV serodiscordant couples based in Thika and Eldoret, Kenya. Data were analyzed from 481 HIV discordant couples enrolled in the Part- ners in Prevention HSV/HIV Transmission Study at the Thika and Eldoret sites. The primary study outcome was self-reported use of contraception other than condoms. Using a marginal longitudinal logistic model based on generalized esti- mating equations (GEE) approach we assessed the association of various demo- graphic and behavioral factors with contraceptive use. At baseline the prevalence of non barrier contraceptive use among HIV positive and negative women was 24.3% and 25.7%, respectively. At month !2 of follow-up, the prevalence of contraceptive use was 44.4% among the HIV positive and 26% among the HIV negative women while at month 24, the prevalence of contraceptive use was 38.6% among the HIV positive and 18.2% among the HIV negative women. HIV positive women were more likely to report using contraception than HIV negative women (odds ratio (OR) 1.61 95% confidence interval (Cl) 1.04-2.47). Addition- ally, being married (OR 2.4, 95% Cl 1.2-5.0), attending Thika site clinic (OR 6.1, 95% Cl 4.2-9.0), and having two or more children (OR 1.9, 95% CI 1.3-2.8) were significantly associated with use of non barrier contraceptives. Future pro- grams should focus on interventions to increase contraceptive use among HIV serodiscordant couples, with a special emphasis on HIV negative women, unmar- ried women and women with few children.