BACKGROUND: The majority of studies that report early life risk factors for pediatric-onset inflammatory bowel disease (IBD) do not account for potential confounding, which can lead to spurious associations and incorrect inferences. AIMS: To assess the relationship between prenatal and perinatal characteristics and the risk of pediatric-onset IBD accounting for potential confounding. METHODS: We conducted a nested case-control study of 189 cases aged =18 years and 3,080 age- and membership-matched controls born at a Kaiser Permanente Northern California facility between 1984 and 2006. The cases were diagnosed with IBD between 1996 and 2006 and diagnosis was confirmed by chart review. We obtained prenatal and perinatal characteristics from the electronic clinical records of the mother and child. Conditional logistic regression was used to assess the associations between these factors and risk of incident IBD, Crohn's disease, and ulcerative colitis. RESULTS: In analyses accounting for confounding, maternal IBD (odds ratio [OR] 5.1, 95 % confidence interval [CI] 2.0-12.9) and white race (OR 2.3, 95 % CI 1.6-3.2) were the only factors statistically associated with pediatric-onset IBD. Maternal respiratory infection during pregnancy (OR 2.0, 95 % CI 1.0-4.0), age < 20 years (OR 2.0, 95 % CI 0.8-4.7) and gestational hypertension (OR 1.7, 95 % CI 1.0-2.7) were associated with pediatric-onset IBD, but did not achieve statistical significance. CONCLUSIONS: Maternal history of IBD and race were the only characteristics of those that we examined that were associated with the development of pediatric IBD in this well-documented population of cases and matched controls.