Background Goal 3.2 from the Sustainable Development Goals (SDG) calls for reductions in national averages of Under-5 Mortality. However, it is well known that within countries these reductions can coexist with left behind populations that have mortality rates higher than national averages. To measure inequality in under-5 mortality and to identify left behind populations, mortality rates are often disaggregated by socioeconomic status within countries. While socioeconomic disparities are important, this approach does not quantify within group variability since births from the same socioeconomic group may have different mortality risks. This is the case because mortality risk depends on several risk factors and their interactions and births from the same socioeconomic group may have different risk factor combinations. Therefore mortality risk can be highly variable within socioeconomic groups. We develop a comprehensive approach using information from multiple risk factors simultaneously to measure inequality in mortality and to identify left behind populations. Methods We use Demographic and Health Surveys (DHS) data on 1,691,039 births from 182 different surveys from 67 low and middle income countries, 51 of which had at least two surveys. We estimate mortality risk for each child in the data using a Bayesian hierarchical logistic regression model. We include commonly used risk factors for monitoring inequality in early life mortality for the SDG as well as their interactions. We quantify variability in mortality risk within and between socioeconomic groups and describe the highest risk sub-populations.