Abstract: Objective The relationship between the seasonal fluctuations in fly density and the incidence of intestinal infectious diseases was investigated to provide basis for implementation of the prevention and control strategies for food-borne diseases. Methods The seasonal fluctuations of fly population and density were monitored using cage traps from 2006 to 2008 in Wenzhou. Data on the incidence of cholera, hepatitis A, hepatitis E, dysentery, typhoid, paratyphoid fever and other intestinal infectious diseases such as diarrhea over the corresponding period in Wenzhou were collected for correlation analysis of the relationship between flies and intestinal infections diseases. Results The major species of flies detected in Wenzhou using cage traps included houseflies (Musca domestica), green flies (Lucilia sericata and Lucilia cuprina) and Chrysomya megacephala, houseflies being the dominant ones. The fly density peaked from June to October with a density of 14.37/cage 6 h. A positive correlation was found between the fluctuations in fly density and the incidence of intestinal infectious diseases, of which flies were positively correlated with infectious diarrhea and typhoid fever (r=0.875, P0.01; r=0.760, P0.01) and correlated to certain degree with cholera, dysentery and paratyphoid (r=0.694, P0.05; r=0.671, P0.05; r=0.616, P0.05), though negatively correlated with hepatitis E (r=-0.616, P0.05) and not correlated with hepatitis A. Conclusion The incidence of intestinal infectious diseases was correlated with the flies in Wenzhou. Therefore, comprehensive control measures should be taken to control the fly density for the prevention and control of intestinal infectious diseases.