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The incidence of Crohn's disease has been increasing in Western communities, but there are no published studies which have examined this change in children in Australia. The centralization of pediatric gastroenterology services in Victoria provides an opportunity to examine these changes within one state.We undertook a retrospective study over a 31-year period of all children aged 16 years or less initially diagnosed with Crohn's disease at either the Royal Children's Hospital, or Monash Medical Center, Melbourne, Victoria.We identified 351 patients who met the diagnostic criteria between 1971 and 2001. The incidence of Crohn's disease in children aged 16 years or less rose from 0.128 to 2.0 per 100 000 per year over the three decades (r = 0.964, P < 0.01). There was a disproportionate over-representation of children from an urban background (incidence rate ratio 1.66, 95% CI 1.28–2.16). Children currently being diagnosed had on average a lower erythrocyte sedimentation rate (ESR) and higher albumin than in previous decades. The use of flexible endoscopy has increased markedly (1970s: 60%; 1990s: 96%, P < 0.05) and the proportion of children recognized at diagnosis with upper gastrointestinal and colonic involvement has increased significantly.There has been a significant increase in the incidence of Crohn's disease in Victorian children. The pattern of disease has also changed with colonic disease now more frequent, and inflammatory indices less abnormal. The increased use of endoscopy has established the frequent involvement of the upper gastrointestinal tract.