Information on the burden of disease due to foodborne pathogens in China is quite limited. To understand the incidence of foodborne gastroenteritis due to non-typhoidal Salmonella enterica and Vibrio parahaemolyticus, population survey and sentinel hospital surveillance were conducted during July 2010 to June 2011 in Shanghai, east China, and a model for calculating disease burden was established. The multiplier for gastroenteritis caused by these pathogens was estimated at 59 [95% confidence interval (CI) 30-102]. Annual incidence per 100,000 population in Shanghai was estimated as 48 (95% CI 24-83) and 183 (95% CI 93-317) cases for foodborne non-typhoidal salmonellosis and V. parahaemolyticus gastroenteritis, respectively, illustrating that bacterial gastroenteritis due to these two pathogens poses a substantial health burden. There is a significant difference between our simulated incidence and the data actually reported for foodborne diseases, indicating significant underreporting and underdiagnosis of non-typhoidal S. enterica and V. parahaemolyticus gastroenteritis in the surveillance area. The present research demonstrates basic situation of the health burden caused by major foodborne pathogens in the surveillance area. Enhanced laboratory-based sentinel hospital surveillance is one of the effective ways to monitor food safety in east China.