Public health education is becoming an increasing priority among educators of medicine. In China, little attention has been paid to public health education reform. A new public health training system was introduced in China in 2007. We conducted this study during 2006-2012 to evaluate the graduate core competencies under the new system. Data were collected from 231 graduates and 49 public health agencies. The 144 graduates who enrolled in 2006 and were trained under the old system constituted the control group; the 87 graduates who enrolled in 2007 and were trained under the new system constituted the experimental group. Surveys of graduate core competencies found analyzing and solving problems in the laboratory, conducting on-site practice and learning new technologies were the top three abilities most expected by public health agencies. After 5-year practical ability training, the graduates in the experimental group had better performance; on-site practical ability and laboratory practical ability increased significantly by 24.5% and 20.0%, respectively. Three other important competencies also improved: designing epidemiologic surveys, collecting information from the literature and doing statistical analyses. However, preventing and controlling common diseases and dealing with emergencies remained weak. These results show the new training system should be continued, but revisions are needed to improve this training system, especially in the areas of preventing and controlling common diseases and dealing with emergencies.

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