The microbiological quality control test for the centers for disease control and prevention was conducted at the provincial, municipal and county level, and the detection capability against six foodborne pathogenic bacteria was evaluate. Methods Six bacteria under test were Listeria monocytogenes, Bacillus cereus, Enterobacter sakazakii, Escherichia coli, Salmonella and Staphylococcus aureus. According to the bacterium combination designed in 2011 and 2012, the samples were prepared by adding the fresh blended culture of pathogenic bacteria into radiation-sterilized milk powder carrier. Six samples of I-VI were prepared in 2011 while ten sample of A-J in 2012. The results of qualification were evaluated using the point-score method. The rate of detection was analyzed with Pearson ² or likelihood ratio². Results The overall qualification rate of 2011 and 2012 were 86.5%(268/310)and 84.3%(375/445), respectively. The lowest qualification rate in 2011 was blank sample VI(68.0%,17/25), while the lowest in 2012 was sample G(0.0%,0/8). In both 2011 and 2012, Escherichia coli was the main false negative bacterium and accounted for 85.7%(60/70)of total false negatives in 2012. The most frequent false positive results among in 2011 were Staphylococcus aureus and Bacillus cereus which were not accounted for the evaluation. In 2012, the highest false positive result was Staphylococcus aureus which accounted for 36.8%(7/19)of the total. In Enterobacter sakazakii and Escherichia coli composite samples of the two years both showed that the false negative rate of Escherichia coli increased significantly. The serotyping accuracy of Salmonella and Escherichia coli were as low as 41.5%(95/229)and 45.1%(105/233), respectively. The false identification occurred on Listeria monocytogenes versus Listeria innocua, Bacillus cereus versus Bacillus mycoides, and Enterobacter sakazakii versus Enterobacter amnigenus. Conclusion More than 80% of the centers possessed qualified detection capability against six foodborne pathogenic bacteria, which satisfied the requirements of food safety risk surveillance. The highest detection capability was toward Salmonella. Staphylococcus aureus had lower false negative results but was easy to produce false positives. The detection capability of Enterobacter sakazakii had improved significantly comparing with the results of 2010.