Introduction The Millennium Development Goals prompted renewed international efforts to reduce under-five mortality and measure national progress. However, scant evidence exists about the distribution of child mortality at low sub-national levels, which in diverse and decentralized countries like India are required to inform policy-making. This study estimates changes in child mortality across a range of markers of inequalities in Orissa and Madhya Pradesh, two of India's largest, poorest, and most disadvantaged states. Methods Estimates of under-five and neonatal mortality rates were computed using seven datasets from three available sources - sample registration system, summary birth histories in surveys, and complete birth histories. Inequalities were gauged by comparison of mortality rates within four sub-state populations defined by the following characteristics: rural-urban location, ethnicity, wealth, and district. Results Trend estimates suggest that progress has been made in mortality rates at the state levels. However, reduction rates have been modest, particularly for neonatal mortality. Different mortality rates are observed across all the equity markers, although there is a pattern of convergence between rural and urban areas, largely due to inadequate progress in urban settings. Inter-district disparities and differences between socioeconomic groups are also evident. Conclusions Although child mortality rates continue to decline at the national level, our evidence shows that considerable disparities persist. While progress in reducing under-five and neonatal mortality rates in urban areas appears to be levelling off, polices targeting rural populations and scheduled caste and tribe groups appear to have achieved some success in reducing mortality differentials. The results of this study thus add weight to recent government initiatives targeting these groups. Equitable progress, particularly for neonatal mortality, requires continuing efforts to strengthen health systems and overcome barriers to identify and reach vulnerable groups.