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Aim To determine if small bowel involvement at diagnosis could predict early relapse in children with ulcerative colitis. Methods Children with newly diagnosed ulcerative colitis were evaluated prospectively at three time points: within 1 month, 6 months and 1 year after diagnosis. Clinical activity indices were used to measure disease activity. Laboratory studies were performed at each visit and/or at the time of relapse. At diagnosis, all patients underwent colonoscopy and a cellobiose/mannitol small intestinal permeability study. Some children were further investigated with an upper gastrointestinal endoscopy. Results Thirty-three patients completed the 1-year study. Overall, nine patients (27.3%) relapsed within 6 months of diagnosis, one patient (3%) within 1 year, whereas 23 patients (69.7%) did not relapse. The mean clinical activity indices, laboratory parameters, extent of colonic involvement, upper and lower gastrointestinal histological features were not predictive of early relapse. Results of the cellobiose/mannitol small intestinal permeability study were significantly higher in children who relapsed within 6 months compared with children who did not relapse (P < 0.013). The cellobiose/mannitol small intestinal permeability study was abnormal in 77.8% of early relapsers compared with only 8.3% of non-relapsers. Conclusion Abnormal small intestinal permeability in children with ulcerative colitis could predict a more relapsing disease.