||Background To compare patterns of healthcare service user preference between urban slums in Dhaka and adjacent rural areas and to identify key determinants of those preferences.Methods The data were collected through baseline surveys conducted in 2008 and 2009. A total of 3207 subjects aged 10–90 years were systematically selected from 12 big slums in Dhaka and 3 rural villages outside Dhaka.Results Two frequently used healthcare sources utilized in 1 month preceding the baseline survey were pharmacies (slum, 42.6%; rural, 30.1%) and government hospitals/clinics (GVHC; slum, 13.5%; rural, 8.9%). According to the multilevel logistic regression analysis adjusted for age, sex and marital status, the likelihood of using pharmacies and GVHC were higher for those subjects who used non-hygienic toilets, who reported food deficiency at a family level, who expressed dissatisfaction about family income and who stated poor health status. Some more factors namely overweight, living in permanently structured house, smoking bidis and less frequency of watching TV were associated with higher likelihood of using GVHC.Conclusions Pharmacy was the most dominant healthcare service in both areas. As persons running pharmacies often provide poor quality of healthcare services, they need continuous training and back-up supports to improve their quality of services and to strengthen the overall healthcare system in Bangladesh.