BACKGROUND: Increasing livestock density and animal manure spreading, along with climate factors such as heavy rainfall, may increase the risk of acute gastrointestinal illness (AGI). In this study we evaluated the association between farming activities, precipitation and AGI. METHODS: A cross-sectional telephone survey of randomly selected residents (n Euro Surveillance (Bulletin Europeen Sur Les Maladies Transmissibles; European Communicable Disease Bulletin) 7006) of 54 rural municipalities in Quebec, Canada, was conducted between April 2007 and April 2008. AGI symptoms and several risk factors were investigated using a phone questionnaire. We calculated the monthly prevalence of AGI, and used multivariate logistic regression, adjusting for several demographic and risk factors, to evaluate the associations between AGI and both intensive farming activities and cumulative weekly precipitation. Cumulative precipitation over each week, from the first to sixth week prior to the onset of AGI, was analyzed to account for both the delayed effect of precipitation on AGI, and the incubation period of causal pathogens. Cumulative precipitation was treated as a four-category variable: high (> or Euro Surveillance (Bulletin Europeen Sur Les Maladies Transmissibles; European Communicable Disease Bulletin) 90th percentile), moderate (50th to <90th percentile), low (10th to <50th percentile), and very low (<10th percentile) precipitation. RESULTS: The overall monthly prevalence of AGI was 5.6% (95% CI 5.0%-6.1%), peaking in winter and spring, and in children 0-4 years old. Living in a territory with intensive farming was negatively associated with AGI: adjusted odds ratio (OR) Euro Surveillance (Bulletin Europeen Sur Les Maladies Transmissibles; European Communicable Disease Bulletin) 0.70 (95% CI 0.51-0.96). Compared to low precipitation periods, high precipitation periods in the fall (September, October, November) increased the risk of AGI three weeks later (OR Euro Surveillance (Bulletin Europeen Sur Les Maladies Transmissibles; European Communicable Disease Bulletin) 2.20; 95% CI 1.09-4.44) while very low precipitation periods in the summer (June, July, August) increased the risk of AGI four weeks later (OR Euro Surveillance (Bulletin Europeen Sur Les Maladies Transmissibles; European Communicable Disease Bulletin) 2.19; 95% CI 1.02-4.71). Further analysis supports the role of water source on the risk of AGI. CONCLUSIONS: AGI poses a significant burden in Quebec rural municipalities with a peak in winter. Intensive farming activities were found to be negatively associated with AGI. However, high and very low precipitation levels were positively associated with the occurrence of AGI, especially during summer and fall. Thus, preventive public health actions during such climate events may be warranted.