As access to antiretroviral therapy increases, more HIV-infected patients in sub-Saharan Africa may desire fertility. We conducted a cross-sectional study of reproductive health knowledge, attitudes and practices to identify factors associated with desired fertility among women and men receiving care at two large public HIV clinics in Lilongwe, Malawi. Research assistants administered questionnaires to participants. We performed descriptive, bivariable and multivariable analysis of factors related to desired fertility and of factors related to contraceptive non-use among participants who did not desire fertility. One-third of participants desired future children. Having a partner who desired fertility and having lower parity were associated with desiring children among both genders. For women, believing that pregnancy was unhealthy was associated with decreased fertility desire. Fifty-five percent of women and 69% of men who did not want children in the future reported using contraception at last intercourse. Increasing age, lower parity, and making the decision to use contraception herself were associated with contraceptive non-use among women who did not desire fertility. Having discussed family planning with his partner was associated with contraceptive use among men who did not desire fertility. Knowledge of these factors can guide reproductive health counseling and service provision.