Using the nationally representative Gender Productivity Survey (GPS) of 2007/08 conducted by the Uganda Bureau of Statistics (UBoS), the paper examines gender biases in school attainment, returns to education, expenditure on health and education, access to health services. While Uganda has recorded progress on MDG 3: promote gender equality and empower women, the paper reveals that significant gender biases still exist with a regional dimension. These biases are more pronounced in Northern Uganda, which is the poorest region. In other words, interventions in this part of the country should be able to address these biases if the region is to catch up with the rest of the country. These findings further suggest that free education both at primary and secondary level; and abolition of user fees in public health facilities is not sufficient for elimination of gender bias. Policies should be based on a better understanding of the households decision making process.