Aims In developed countries, the incidence of inflammatory bowel disease (IBD) such as Crohn's disease (CD) and ulcerative colitis (UC) is increasing. Therefore, we aimed to investigate the incidence rates and trends over time in the population of children and adolescents in one of the federal states of Germany, in Saxony. Methods Over the 10-year period 2000–2009 all 31 children’s hospitals and pediatric gastroenterologists, respectively in Saxony reported all IBD patients up to 15 years of age to the Saxon Pediatric IBD Registry. The completeness of the registry was estimated as 96.7% by independent surveys in the years 2005–2009. Incidence rates were presented as age-standardized incidence rates (ASR) regarding New European Standard Population 1990 per 100,000 person-years (PY) with 95% confidence intervals [CI]. Joinpoint and linear regression was used for trend analyses. Results 344 patients with confirmed IBD between 2000–2009 were included in the epidemiological evaluation: 212 (61.6%) patients with CD, 122 (35.6%) with UC and 10 (2.9%) with unclassified IBD (IBD-U). The ASR per 100,000 PY over the whole observation period was 7.2 [6.4–7.9] for IBD, 4.4 [3.8–5.0] for CD, 2.6 [2.1–3.0] for UC and 0.2 [0.1–0.3] for IBD-U. For IBD, the ASR per 100,000 PY increased from 4.6 [2.8–6.3] in 2000 to 10.5 [7.5–13.6] in 2009. The incidence trend analysis of ASRs using the joinpoint regression confirmed a significant increase of IBD as well as UC. The mean age at first diagnosis decreased significantly during the observation period from 11.5 (11.0–13.4) in 2000 to 9.6 (5.1–13.5) years in 2009. The median of the diagnostic latency among IBD patients was 3 months. Conclusion The incidence of IBD in children and adolescents in Saxony was slightly higher than the average of other countries in the same time period and followed the trend towards a general increase of IBD. The age at diagnosis was subject to a very unfavorable downward trend.