BACKGROUND: The Chinese Ministry of Health (MOH) and the United Nations Children's Fund (UNICEF) carried out the Rural Primary Health Care Project (RPHC) with a government-led, province-level, integrated intervention that targeted children under 3 years old in rural areas of western China from 2001 to 2005. The objective of this study was to measure the effectiveness of the intervention on childhood nutrition. METHODS: 10 415 and 9916 children under 3 years old in 2001 and 2005, respectively, were selected in rural areas of western China. Stunting was used as the sole outcome variable to assess the child undernutrition change over time. The concentration index was used to assess the extent of the inequality of child undernutrition. Difference-in-difference estimation was used to evaluate the effects of the intervention on child undernutrition. RESULTS: After the intervention, the proportion of child stunting decreased from 20.8% to 10.2%. The results from the difference-in-difference estimation with stunting adjusting for socio-demographic characteristics showed that the intervention had significantly improved the child stunting rate by 0.4%. Despite the decline in the undernutrition rate, the concentration indices for stunting in the intervention group decreased from -0.139 to -0.223 between 2001 and 2005. CONCLUSION: This intervention project was effective in reducing childhood undernutrition rates to some extent in rural areas of western China. However, it seems that the project had a negative effect on the equity of undernutrition.