Objective To understand the laboratory testing capabilities of disease prevention and control institutions in Beijing, compare them with other provincial or municipal disease prevention and control institutions in China, analyze the existing problems, and provide evidence for capacity building of disease prevention and control institutions in Beijing.

Methods A questionnaire survey of laboratory testing capabilities was conducted in the municipal and 18 district centers for disease control and prevention (CDCs) in Beijing, and in 13 provincial (municipal) and 190 prefectural CDCs.

Results The overall coverage rate of laboratory testing in pathogen detection was 97.93% in the municipal CDC and the average coverage rate in the district CDCs was 31.61% (0.21%−44.21%, <30.00% in 7 district CDCs) in Beijing. There were significant differences in the coverage rate among the district CDCs in Beijing (P<0.001), as well as between the municipal CDC and the district CDCs in Beijing (P<0.001). The total coverage rate of laboratory testing in the municipal CDC of Beijing was higher than the average coverage rate in 14 provincial (municipal) CDCs (73.55%) and three municipal CDCs (86.50%). The average coverage rate in 18 district CDCs in Beijing was lower than the average coverage rate of 208 prefectural (district) CDCs in other provinces (41.07%). The coverage rate of laboratory testing was 100.00% for microorganism detection and 97.03% for physicochemical detection in the mingunicipal CDC of Beijing. The average coverage rates of laboratory testing in microorganism and physicochemical detections in the district CDCs of Beijing were 42.17% and 27.00%, respectively. The coverage rate in pathogenic microorganism detection in the municipal CDC of Beijing was 100.00%, while the coverage rates in all other provincial (municipal) CDCs was >80.00%. However, the average coverage rate was 54.13% in prefectural (district) CDCs in other provinces, and only 42.90% in the district CDCs of Beijing. In the 101 pathogenic microorganism testing surveyed, 85 had an average coverage rate of ≥10% in CDCs at all levels, but 8 had not been conducted in municipal and district CDCs in Beijing, all belonged to physicochemical testing.

Conclusion The coverage rate of laboratory testing in pathogen detection was higher in the inmunicipal CDC of Beijing than in other provincial (municipal) CDCs surveyed. However, the coverage rate were lower in the district CDCs of Beijing than in other prefectural (district) CDCs surveyd. The developments of laboratory testing capability building in all the district CDCs of Beijing were not balanced. It is necessary to sthengthen the capabiloty build of laboratory testing in local district CDCs to improve disease prevention and control, and protect people’s health in Beijing.