Objective The purpose of the study was to investigate the trends and causes of regional disparities of infant mortality rate (IMR) in rural China from 1996 to 2008.

Design A population-based, longitudinal study.

Setting The national child mortality surveillance network.

Population Population of the 79 surveillance counties.

Main outcome measure IMR, leading causes of infant death and the RR of IMR.

Results The IMR in coastal, inland and remote regions declined by 72.4%, 62.9% and 58.2%, respectively, from 1996 to 2008. Compared with the coastal region, the RR of IMR were 1.7 (95% CI 1.6 to 1.9), 1.9 (95% CI 1.7 to 2.0) and 1.8 (95% CI 1.6 to 2.0) for inland region and 2.6 (95% CI 2.4 to 2.7), 3.2 (95% CI 3.0 to 3.5) and 3.1 (95% CI 2.7 to 3.4) for the remote region during 1996–2000, 2001–2005 and 2006–2008, respectively. The regional disparities existed for both male and female IMRs. The postneonatal mortality showed the highest regional disparities. Pneumonia, birth asphyxia, prematurity/low birth weight, injuries and diarrhoea were the main contributors to the regional disparities. There were significantly more infants who did not seek healthcare services before death in the remote region relative to the inland and coastal regions.

Conclusion The results indicated persistent existence of regional disparities in IMR in rural China. It is worth noting that regional disparities in IMR increased in the remote and coastal regions during 2001–2005 in rural China. These disparities remained unchanged during 2006–2008. The results indicate that strategies to reduce mortality caused by pneumonia, birth asphyxia and diarrhoea are keys to reducing IMR.