BACKGROUND: An individual's intestinal bacterial flora is established soon after birth. Delivery by Cesarean section (c-section) deprives the newborn of colonization with maternal vaginal bacteria. We determined whether delivery by c-section is associated with an altered risk of infection with intestinal bacterial pathogens. METHODS: In a cohort of 1.7 million Danes born 1973-2005 we identified cases of laboratory-confirmed non-typhoidal Salmonella species, Campylobacter species, Yersinia enterocolitica, Shigella species, and Shiga toxin-producing Escherichia coli from 1991-2005 in the National Registry of Enteric Pathogens. Using Poisson-regression we estimated confounder-adjusted incidence rate ratios (IRRs) for infection according to mode of delivery. RESULTS: During 14.0 million person-years of follow-up, 22,486 individuals were diagnosed with 1 intestinal bacterial infection. C-section was associated with a small increase in risk at age 1 to