BACKGROUND: For many low and middle-income countries poor quality health care is now responsible for a greater number of deaths than insufficient access to care. This has in turn raised concerns around the distribution of quality of care in LMICs: do the poor have access to lower quality health care compared to the rich? The aim of this study is to investigate the extent of inequalities in the availability of quality health services across the Indonesian health system with a particular focus on differences between care delivered in the public and private sectors. METHODS: Using the Indonesian Family Life Survey (wave 5, 2015), 15,877 households in 312 communities were linked with a representative sample of both public and private health facilities available in the same communities. Quality of health facilities was assessed using both a facility service readiness score and a knowledge score constructed using clinical vignettes. Ordinary least squares regression models were used to investigate the determinants of quality in public and private health facilities. RESULTS: In both sectors, inequalities in both quality scores existed between major islands. In public facilities, inequalities in readiness scores persisted between rural and urban areas, and to a lesser extent between rich and poor communities. CONCLUSION: In order to reach the ambitious stated goal of reaching Universal Health Coverage in Indonesia, priority should be given to redressing current inequalities in the quality of care.