Objective: To establish an emergency response capability assessment indexes for disease control and prevention institutions. Methods: Health emergency response capability assessment indexes of Shanghai Centers for Disease Control and Prevention(CDCs) was drafted based upon documentary analysis, expert consultation and focus group discussion according to duties and features of emergency work of CDCs. The assessment indexes were determined by applying Delphi method (18 experts), and the weights of indexes were determined using analytic hierarchy process and proportional distribution method. And then the established index system was used to assess the emergency response capability of CDCs in Shanghai. Results: Two rounds of expert consultations were conducted. Kendall's coefficient of concordance was 0.420 and 0.495 at the first and second round of expert consultations respectively. After two rounds of consultations, the expert authority score was above 0.7. There were 7 primary indexes, 24 secondary indexes and 84 third-level indexes. The seven primary indexes included emergency management system, emergency response team, surveillance and early-warning ability, emergency response capacity, emergent supply capability, communication and cooperation, scientific research and exchange, with systematic weights of 0.2123, 0.1754, 0.1334, 0.1916, 0.1281, 0.0962 and 0.0630, respectively. According to the investigation, Shanghai Municipal Center for Disease Control and Prevention ranked first in the total score of emergency response capability evaluation. Conclusion: The indexes identified in this study have good reliability and feasibility, and can be used in assessment of emergency response capability in disease prevention and control institutions.