Background and Aims Few epidemiological investigations characterize inflammatory bowel disease (IBD) in non-Caucasian children. Our study compared IBD characteristics between African-Americans and non-African-Americans enrolled in a multi-center pediatric IBD registry with endoscopic- and pathology-based diagnosis. Methods The study retrieved data entered from January 2000–October 2003 on children 1 to 17 years old, inclusive, followed by a consortium of academic and community U.S. pediatric gastroenterology practices. Analyses examined racial/ethnic differences by comparing the proportions of African-Americans and non-African-Americans in: each diagnostic disease classification (any IBD, Crohn's disease, ulcerative colitis, indeterminate colitis); age group (<6y, 6–12y or >12y) at diagnosis or symptom onset; presence of extraintestinal manifestations, Z-scores for height and weight, immunomodulatory therapy, anatomic disease location and abnormal hemoglobin, albumin or sedimentation rate at diagnosis. Results 1,406 patients had complete data, 138 (10%) of whom were African-American. African-Americans more often: were >12y of age at diagnosis (52% vs. 37%, OR 1.82, 95% CI 1.28–2.59) and symptom onset (46% vs. 30%, OR 1.99, 95% CI 1.40–2.84); had Crohn's disease (78% vs. 59%, OR 2.36, 95% CI 1.56–3.58); had low hemoglobin at diagnosis (39% vs. 17%, OR 3.15, 95% CI 1.92–5.17). Conclusions IBD in African-American children and adolescents presents more commonly with CD and at older ages compared to non-African-Americans. Racial/ethnic differences in the epidemiology of IBD, particularly CD, among American youths require further investigation.