Abstract: Objective To assess the efficiency of centers for disease control and prevention(CDCs)at county-level in China and for making strategies to improve the performance of the CDCs.Methods A total of 416 county-level CDCs were selected with systematic sampling.Data envelopment analysis(DEA)framework was used to estimate overall,technical and scale efficiency of the CDCs in 2012 and projection analysis was conducted to identify the difference between projection value and actual value for inputs and outputs.Results The average overall efficiency score of the CDCs was 0.505 and the average technical efficiency score was 0.687.A progressive decrease in return to scale was observed for 87.98%of the CDCs.Projection analysis indicated that 7 categories of outputs were under-produced.To achieve DEA efficiency,public emergency management(188.5%),health education(165.7%),and laboratory tests(163.6%)are the first 3 aspects to be promoted for its output.Conclusion Most county-level CDCs in China are currently operated inefficiently and the utilization of the resources is not sufficient in the CDCs.The proportion of governmental funding to manpower and general expenditure should be increased to promote the output efficiency of resources.