More than 150 million women become pregnant in developing countries annually and an estimated 287,000 die from pregnancy-related causes. Contraception is vital to prevent unnecessary maternal deaths, as well as sexually transmitted infections. The objective of this study was to investigate preferred contraceptive methods and the factors that influence contraceptive choice among women in Kelantan, Malaysia. A cross-sectional study using interview-based questionnaires was conducted, during July and August 2009, in local family planning clinics in Kelantan. The questionnaire was administered to female adults (age 20–50). Data were analysed using SPSS v15.0. Prevalence of unplanned pregnancies was high (48%). Contraceptive preference was Depo contraceptive injection (32%), oral contraceptive pills (27%), intrauterine devices (15%) and contraceptive implants (12%); 9% used condoms. Only 2% used contraception to protect against sexually transmitted infections or HIV/AIDS. Younger women (OR 0.90; 95% CI 0.807–0.993) were more likely to use contraception. In conclusion, non-interrupted contraceptive methods were preferred. More than 60% would stop using contraception if it interrupted intercourse. From both a public health and infectious disease perspective, this is extremely worrying.