Introduction: Globally every year 529,000 maternal deaths occur, 99% of this in developing countries. Uganda has high maternal and neonatal morbidity and mortality ratios, typical of many countries in sub-Saharan Africa. Recent findings reveal maternal mortality ratio of 435:100,000 live births and neonatal mortality rate of 29 deaths per 1000 live births in Uganda; these still remain a challenge. Women in rural areas of Uganda are two times less likely to attend ANC than the urban women. Most women in Uganda have registered late ANC attendance, averagely at 5.5 months of pregnancy and do not complete the required four visits. The inadequate utilization of ANC is greatly contributing to persisting high rates of maternal and neonatal mortality in Uganda. This study was set to identify the factors associated with late booking and inadequate utilization of Antenatal Care services in upcountry areas of Uganda. Method: Cross-sectional study design with mixed methods of interviewer administered questionnaires, focus group discussions and key informant interviews. Data was entered using Epidata and analyzed using Stata into frequency tables using actual tallies and percentages. Ethical approval was sought from SOM-REC MakCHS under approval number "#REC REF 2012-117" before conducting the study. Results: A total of four hundred one were enrolled with the majority being in the age group 20 -24 years (mean age,