The study aimed to analyze reasons for the use or non-use of antenatal care services and malaria treatment among pregnant women living in rural areas in Uganda. Focus group discussions with pregnant women, in-depth interviews with key informants (Traditional Birth Attendants (TBAs) and health workers) and a structured questionnaire administered to pregnant women were used to collect the relevant information. Antenatal care attendance was irregular and few women knew that the purpose of attending antenatal care was to monitor both the growth of the baby and the health status of the woman. Parity significantly influenced antenatal care attendance, but level of education, religion and marital status did not. Fifty-five per cent of the women stated that they had delivered outside the formal health delivery system despite antenatal care attendance. All women in their second pregnancy had delivered their first child in the village, despite TEA training to the contrary. Malaria as perceived by pregnant women is common and multiple health service providers are used for its treatment. About 66% of the mothers reported having suffered from malaria during the current pregnancy; of these more than half had received treatment outside the formal health delivery system. Self-treatment with drugs bought from ordinary shops was commonly reported. Nearly all women (93.3%) knew about the antimalarial drug chloroquine and 83% thought that it was used for the treatment of malaria, not for its prevention. Some women believed that the drug could cause abortion. Health seeking behaviour was influenced by several factors, including the perceived high cost of antenatal care services, of conducting a delivery and treatment, and perceived inadequacy of services provided by the formal health system. Inadequacy of formal health services was perceived by users to be partly due to understaffing and to irregular supply of essential drugs. Intensive health education to pregnant women on the safety of chloroquine use in pregnancy, the importance and the need for regular antenatal care attendance are recommended. In addition, training of more TBAs and continued educational efforts to upgrade their knowledge, regular and adequate supply of essential drugs, and free health services for high-risk groups such as pregnant women are recommended to improve antenatal care services and drug prophylaxis use in pregnancy.