Objective To estimate provincial, regional and national newborn screening coverage throughout China. Method Information about newborn screening was collected using a survey questionnaire from neonatal screening laboratories in China in 2006–2007. The total number of live births at the provincial and national levels was obtained from the Maternal and Child Health Information System (MCHIS) and the State Statistics Bureau (SSB), respectively, and was used to calculate the neonatal screening coverage at the provincial, regional and national levels. Results There were 185 laboratories providing neonatal screening services in China in 2007. The rates of national screening coverage in 2006 and 2007 were 31.27% and 39.96%, respectively, based on live birth numbers reported by the SSB. Both of these estimates are lower than those calculated from live birth numbers reported by the MCHIS. The rates of coverage in the Eastern, Middle and Western regions were about 84.90%, 30.41% and 19.82%, respectively, based on the live birth numbers reported by the MCHIS. Conclusion There are disparities in screening coverage between regions and between provinces throughout China, but the extent of this is difficult to ascertain because of the different systems of reporting live births. To calculate nationwide screening coverage it is probably appropriate to use the SSB data on live births. However, for provincial screening coverage the calculation is probably best based on the number of live births reported by the MCHIS once the validity of the MCHIS data is verified.