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Lactase deficiency is commonly found in adults with inflammatory bowel disease (IBD). Our aim was to determine its prevalence in children with IBD.We conducted a retrospective and descriptive analysis of patients with symptomatic IBD whose mucosal lactase activity was measured on duodenal biopsies obtained during gastrointestinal endoscopic evaluations. Age- and gender-matched controls were chosen randomly from a group with chronic abdominal pain.One hundred twelve patients with IBD were identified from January 1994 to December 2000. Seventy-nine (71%) had Crohn disease, and 33 (29%) had ulcerative colitis. Forty-five (40%) of all IBD patients (29 with Crohn disease and 16 with ulcerative colitis) had low lactase activity levels (< 15 μM/min/gm). The prevalence of lactase deficiency in patients with IBD was 37% (38 of 103) in white patients and 78% (7 of 9) in blacks. Thirty-four of 112 controls (30%) had lactase deficiency. IBD patients were more likely to be lactase deficient than the controls, but the difference was not statistically significant (P = 0.162). Normal duodenal histology was found in 67% of lactase-deficient IBD patients compared with 82% in lactase-sufficient IBD patients. The frequency of duodenal inflammation did not differ significantly between lactase-deficient and -sufficient patients with IBD (P = 0.068).More than one third of pediatric patients with IBD have lactase deficiency, which is not significantly different from non-IBD patients with chronic abdominal pain. The majority of lactase-deficient patients with IBD have normal duodenal biopsy results. Lactase activity from small bowel biopsy specimens can be measured at the time of initial endoscopy. Reevaluation, either by small bowel biopsy or the breath hydrogen test, may then be considered during follow-up of symptomatic patients.