More than 90% of pediatric AIDS results from the transmission of the virus through HIV positive pregnant mothers to their children. However, little has been known about factors associated with unintended pregnancies after knowing their HIV seropositive status, or contraceptive use among HIV positive women under antiretroviral treatment (ART). We investigated thus factors associated with unintended pregnancies after knowing seropositive status, and also factors associated with the non-use of contraceptives among HIV positive women under ART. We carried out a cross-sectional study in Kigali, Rwanda in 2007. A total of 565 HIV positive women under ART were interviewed. We examined the associated factors of unintended pregnancies or non-use of contraceptives using logistic regression analysis. Among all the respondents (n = 565), 132 women became pregnant after knowing their HIV seropositive status. Among them, 82 (62.7%) got pregnant unintentionally. Those who had two or more children (adjusted OR, 3.83) were more likely to get pregnant unintentionally. Meanwhile, among all, 263 had sexual intercourse during the last three months. Of them, 85 women did not use any contraceptives. Those who did not agree that 'HIV positive children can survive as long as HIV negative children' (adjusted OR, 2.28), and those who 'can always ask partner to use a condom' (adjusted OR, 9.83), were more likely to use contraceptives. This study suggests that HIV positive women under ART need special support to avoid unintended pregnancies especially those who have two or more children. Moreover, interventions are also needed to improve women's understanding of the prognosis of pediatric AIDS, and condom-use negotiation skills.