The incidence of inflammatory bowel disease (ibd) is rising. Incidence studies could provide more insight into etiological factors. The aim of this study was to prospectively assess the incidence of paediatric ibd in the Netherlands from 1999 to 2001, using both an active physician case reporting registry and a nation-wide pathology database. All paediatricians in the Netherlands were monthly asked to report any newly diagnosed ibd cases. A national pathology database which contains reports from all cytological and histological diagnoses in the country was searched for new cases. Cases identified from the pathology database were labeled as ‘probable ibd’ or ‘possible ibd’. Cases were cross-checked across databases on the basis of sex, date of birth, date of biopsy and place of residence. 546 Probable cases of ibd were identified, 217 were labeled as possible cases. The incidence rate was 7.2 new cases per 100,000 children per year. An increase in incidence with age was observed. Only 24% of the cases were ascertained through the clinical registry. The incidence of ibd cases in the Netherlands is comparable to that reported in other European countries. Epidemiological studies using only case reporting by physicians may underestimate true incidence rates.