Background In 2009, China implemented the National Essential Medicines System (NEMS) to improve access to high-quality low-cost essential medicines. Objective To measure the prices, availability and affordability of medicines in China following the implementation of the NEMS. Setting 120 public hospitals and 120 private pharmacies in ten cities in Shaanxi Province, Western China. Method The standardized methodology developed by the World Health Organization and Health Action International was used to collect data on prices and availability of 49 medicines. Main outcome measures Median price ratio; availability as a percentage; cost of course of treatment in days’ wages of the lowest-paid government workers. Results In the public hospitals, originator brands (OBs) were procured at 8.89 times the international reference price, more than seven times higher than the lowest-priced generics (LPGs). Patients paid 11.83 and 1.69 times the international reference prices for OBs and generics respectively. A similar result was observed in the private pharmacies. The mean availabilities of OBs and LPGs were 7.1 and 20.0 % in the public hospitals, and 12.6 and 29.2 % in the private pharmacies. Treatment with OBs is therefore largely unaffordable, but the affordability of the LPGs is generally good. Conclusion High prices and low availability of survey medicines were observed. The affordability of generics, but not OBs, is reasonable. Effective measures should be taken to reduce medicine prices and improve availability and affordability in Shaanxi Province.