Indonesia's rapidly growing mega-urban regions of Jabodetabek (Jakarta Extended Metropolitan Region), Bandung and Surabaya each have a large and socio-economically heterogeneous population. The 2000 Census presents evidence that substantial spatial and socio-economic inequalities in under-five mortality risk exist in these mega-urban regions. Differences in patterns of birth attendant utilization likely contribute to these inequalities. Multilevel multinomial logistic regression of data primarily from the National Socio-economic Survey (SUSENAS) reveals that use of a skilled birth attendant is highly associated with mother's education. Highly skilled assistance is more related to the enabling factor of household expenditure quintile. The findings provide evidence for efforts to help reduce inequalities in early age mortality risk through improved access to trained birth assistance, in addition to other interventions.