BACKGROUND: Enabling women living with HIV to effectively plan whether and when to become pregnant is an essential right; effective prevention of unintended pregnancies is also critical to reduce maternal morbidity and mortality as well as vertical transmission of HIV. The objective of this study is to examine the use of family planning (FP) services by HIV-positive and HIV-negative women in Kenya and their ability to achieve their fertility desires. METHODS: Data are derived from a random sample of women seeking family planning services in public health facilities in Kenya who had declared their HIV status (1887 at baseline and 1224 at endline) and who participated in a longitudinal study (the INTEGRA Initiative) that measured the benefits/costs of integrating HIV and sexual/reproductive health services in public health facilities. The dependent variables were FP use in the last 12 months and fertility desires (whether a woman wants more children or not). The key independent variable was HIV status (positive and negative). Descriptive statistics and multivariate logistic regression analysis were used to describe the women's characteristics and to examine the relationship between FP use, fertility desires and HIV status. RESULTS: At baseline, 13 % of the women sampled were HIV-positive. A slightly higher proportion of HIV-positive women were significantly associated with the use of FP in the last 12 months and dual use of FP compared to HIV-negative women. Regardless of HIV status, short-acting contraceptives were the most commonly used FP methods. A higher proportion of HIV-positive women were more likely to be associated with unintended (both mistimed and unwanted) pregnancies and a desire not to have more children. After adjusting for confounding factors, the multivariate results showed that HIV-positive women were significantly more likely to be associated with dual use of FP (OR = 3.2; p < 0.05). Type of health facility, marital status and household wealth status were factors associated with FP use. Factors associated with fertility desires were age, education level and household wealth status. CONCLUSIONS: The findings highlight important gaps related to utilization of FP among WLHIV. Despite having a greater likelihood of reported use of FP, HIV-positive women were more likely to have had an unintended pregnancy compared to HIV-negative women. This calls for need to strengthen family planning services for WLHIV to ensure they have better access to a wide range of FP methods. There is need to encourage the use of long-acting reversible contraceptive (LARC) to reduce the risk of unintended pregnancy and prevention of vertical transmission of HIV. However, such policies should be based on respect for women's right to informed reproductive choice in the context of HIV/AIDS. TRIAL REGISTRATION: NCT01694862.