Objective To investigate and identify the contamination of main foodborne pathogenic bacteria and the kind of high-risk foods and to provide scientific basis for prevention and control of foodborne diseases in Jiangsu Province. Methods Based on the standard operation procedures in the handbook of National Surveillance on Foodborne Pathogenic Bacteria, 3865 food samples from 13 cities in Jiangsu Province from 2006 to 2009 were collected and analyzed for the occurrence of Salmonella, Listeria monocytogenes, Vibrio parahaemolyticus, Staphylococcus aureus, Campylobacter jejuni and Escherichia coli O157 in foods. Results Of the 3865 food samples tested, 490 (12.68%) pathogenic strains were isolated. The positive rate of foodborne bacterial pathogens in raw meat, raw milk, aquatic products, quick-frozen flour and rice products, cooked meat, cakes and vegetable salad were 27.93% (242/814), 18.87% (10/53), 17.49% (89/509), 16.18% (56/346), 9.24% (56/606), 4.79% (7/146) and 0.98% (5/509), respectively. The positive rate of foodborne bacterias from 2006 to 2009 was 16.92%, 14.05%, 15.32%, 7.06%, respectively. Among the 13 cities, the positive rate in Taizhou, Nanjing, Yangzhou and Xuzhou were higher in comparison with other cities. Conclusion Raw meat, raw milk and aquatic food products are the main kinds of food contaminated by foodborne pathogens in Jiangsu province. As the ready-to-eat food, such as cooked meat, aquatic products eaten in raw and cakes are at higher risks for causing foodborne diseases.