BACKGROUND Antenatal care (ANC) aims mainly at prevention, early detection and management of general medical and pregnancy associated disorders. Early booking is recommended for maximum utilisation. OBJECTIVE To investigate the determinants of first ANC visit and trimesters at which pregnant mothers enrol for ANC at the COBERS sites of Northern Uganda. DESIGN A descriptive cross-sectional study. SETTING Five community based Education, Research and Service sites (COBERS) of Atiak, Madi Opei, Mungula, Namukora and Pajule health centre, fours (HC IV) in the five respective districts of Amuru, Lamwo, Adjumani, Kitgum and Pader, Northern Uganda, from April to July 2013. SUBJECTS Four hundred and seventeen (417) pregnant women attending antenatal care (ANC) in five health centres and ten purposively selected midwives were interviewed using questionnaires. RESULTS Of the 417 respondents, only 11.5% (n = 48) had their first ANC at the recommended period of 0-16 weeks. Prevalence of late entry to ANC was 88.5% (n = 369). Mean gestational age at booking was 22.6 ± 5.7 weeks. Paternal level of education, outcome of previous pregnancy, previous ANC attendance, weeks of amenorrhea, convenience of opening hours at ANC facility, commuting distance from home to health facility, knowing the right time for ANC enrollment and pregnancy planning remained significant predictors governing early booking. CONCLUSION Late ANC booking is still a major public health concern that demands public enlightenment and paternal education coupled with women empowerment will reduce the magnitude of the problem.