To evaluate associations between indicators of livestock farming intensity (manure surplus and livestock density) and acute gastroenteritis hospitalization (AGH) rate, we conducted an ecological study on 306 selected agricultural municipalities of Quebec. We estimated the AGH rate for the period 2000–2004 from the Quebec hospital database. Multivariate Poisson regression was used to estimate the strength of association between the farming indicators and AGH with adjustment for confounders. The modifying effect of age and water source was also evaluated. Association between manure and AGH was observed in children, especially those aged 0–4 years for selected zoonotic infections [adjusted hospitalization rate ratio (aHRR) 1·93, 95% CI 1·21–3·09]. The risk ratio was higher for subjects using ground-water source. An increasing HRR trend with each additional level of poultry density was observed in children aged 0–4 years, especially for Salmonella infections. We conclude that livestock farming intensity may be linked to bacterial acute gastroenteritis in children.