Objective To obtain the data of food-borne disease incidence from a multipurpose surveillance in Shanghai. Methods Active symptom surveillance of food-borne diarrhea in community residents, rectal swab test for diarrhea outpatients in hospitals, the absence of students from diarrhea in primary and middle schools, the sale of berberine and norfloxacin in pharmacies and the reports of food poisoning outbreak from networks were applied. Results The incidence of food-borne diarrhea in Shanghai community residents was 2.62% and the rate of visiting doctors was 40.2%. The positive rate of Salmonella and Vibrio parahaemolyticus from rectal swabs in diarrhea outpatients were 2.95% and 0.53%, respectively. The absence rate from diarrhea in primary and middle school students were 1.59% and 1.00% respectively. Berberine and norfloxacin sold in pharmacies were 81157 packages (￥374449 RMB) and 21416 packages (￥80927 RMB) respectively. Sixteen outbreaks of food poisoning involving 488 people were reported. The results of the surveillance showed that the peak of food-borne diarrhea incidence from May to October was also the peak of positive rate of Vibrio parahaemolyticus. Conclusion The surveillance of food-borne disease in Shanghai generally reflected the low incidence of food-borne disease in Shanghai. But the surveillance system in defining objects of monitoring and quality control should be improved.