Background Inflammatory bowel disease (IBD) is rare in Asian children and few reports on pediatric IBD have appeared. Aims We, therefore, investigated the incidence trends and clinical characteristics of pediatric IBD in Korea. Methods We enrolled 48 children with Crohn's disease (CD) and 14 children with ulcerative colitis (UC) from 1996 to 2007. Trends in annual enrollment and clinical characteristics were retrospectively evaluated by medical record review. Results During the 12 years of observation, the number of new enrollments gradually increased. CD showed male predominance (33 boys, 15 girls), but more females presented with UC (4 boys, 10 girls). A relevant family history was observed in 3 (4.9%) of the 61 unrelated families. The most common presenting symptom was abdominal pain (67%) in CD and hematochezia (93%) in UC. Growth delay was observed in 10% of CD patients, but not in any of the UC patients. In CD, colonic involvement occurred in 87% of patients, ileal involvement in 87%, and both the small bowel and colon were affected in 75%. With UC, pancolitis occurred in 43% of patients, left-sided colitis in 36%, and proctitis in 21%, including all three patients with appendiceal orifice inflammation. The most frequent disease behavior was inflammatory in 85% of patients, but perianal fistula was noted in 50% of CD patients. Conclusion This study showed that the incidence of pediatric IBD has been rapidly increasing in Korea in recent years. Relevant family history is less prevalent and phenotypic expression differs from what is seen in Western countries.