The aim was to evaluate the incidence, treatment, surgery rate, and anthropometry at diagnosis of children with inflammatory bowel disease (IBD). Patients diagnosed between January 1, 2007 to December 31, 2009 in Eastern Denmark, Funen, and Aarhus were included from a background population of 668,056 children <15 years of age. For evaluation of incidence, treatment, and surgery rate, a subcohort from Eastern Denmark was extracted for comparison with a previously published population-based cohort from the same geographical area (1998-2006). In all, 130 children with IBD: 65 with Crohn's disease (CD), 62 with ulcerative colitis (UC), and three with IBD unclassified (IBDU) were included. The mean incidence rates per 10(6) in 2007-2009 were: IBD: 6.4 (95% confidence interval [CI]: 5.4-7.7), CD: 3.2 (2.5-4.1), UC: 3.1 (2.4-4.0) and IBDU: 0.2 (0.05-0.5). Comparing the two cohorts from Eastern Denmark we found higher incidence rates for IBD (5.0 and 7.2 in 1998-2000 and 2007-2009, respectively, P = 0.02) and CD (2.3 versus 3.3, P = 0.04). Furthermore, we found a significant decrease in surgery rates (15.8/100 person-years versus 4.2, P = 0.02) and an increase in the rate of initiating immunomodulators (IM) within the first year (29.0/100 person-years versus 69.2, P < 0.001). IM use was associated with a trend towards a decreased surgery risk (relative risk [RR] 0.38; 0.15-1.0). Children with CD had poor nutritional status at diagnosis compared with the general pediatric population. Over the past 12 years we found an increase in the incidence of IBD in children, an increasing use of IM, and decreasing 1-year surgery rates. CD patients had poor nutritional status. Copyright © 2011 Crohn's & Crohn's & Colitis Foundation of America, Inc.