Socio-economic disparities in health have been well documented around the world. This study examines whether NGO facilitation of the government's community-based health programme improved the equity of maternal and newborn health in rural Uttar Pradesh, India. A quasi-experimental study design included one intervention district and one comparison district of rural Uttar Pradesh. A household survey conducted between January and June 2003 established baseline rates of programme coverage, maternal and newborn care practices, and health care utilization during 2001-02. An endline household survey was conducted after 30 months of programme implementation between January and March 2006 to measure the same indicators during 2004-05. The changes in the indicators from baseline to endline in the intervention and comparison districts were calculated by socio-economic quintiles, and concentration indices were constructed to measure the equity of programme indicators. The equity of programme coverage and antenatal and newborn care practices improved from baseline to endline in the intervention district while showing little change in the comparison district. Equity in health care utilization for mothers and newborns also showed some improvements in the intervention district, but notable socio-economic differentials remained, with the poor demonstrating less ability to access health services. NGO facilitation of government programmes is a feasible strategy to improve equity of maternal and neonatal health programmes. Improvements in equity were most pronounced for household practices, and inequities were still apparent in health care utilization. Furthermore, overall programme coverage remained low, limiting the ability to address equity. Programmes need to identify and address barriers to universal coverage and care utilization, particularly in the poorest segments of the population.