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Recent evidence points toward an active immunological role of intra-abdominal adipose tissue in Crohn disease (CD). We quantified the abdominal adipose tissue compartments using magnetic resonance imaging (MRI) in 27 pediatric patients with CD compared with 14 controls undergoing MRI examination for other reasons.Total (TAAT), subcutaneous (SCAT) and intra-abdominal (IAAT) adipose tissue areas were measured by semiautomatic segmentation on a transverse slice centered on the umbilicus (mean ± standard deviation in square centimeter) using standard T1-weighted sequences. IAAT/TAAT and IAAT/height ratios were calculated and analyzed for associations with disease duration, phenotype, or therapy.Patients with CD (median age 15.0 years, range 7.7–17.9, 18/27 boys, median disease duration 29 months, range 0–136) compared to controls (median age 13.9 years, range 3.3–17.8, 4/14 boys) had higher IAAT area (42.3 ± 21.0 vs 28.7 ± 11.6, P = 0.0494) but similar SCAT and TAAT areas (104.6 ± 72.8 vs 96.5 ± 50.8, P = 0.8170 and 146.9 ± 87.3 vs 125.3 ± 61.5, P = 0.7417, respectively). IAAT/TAAT ratio was higher in patients with CD compared to controls (0.32 ± 0.10 vs 0.24 ± 0.04, P = 0.0081). Patients with disease duration >2 years (n = 14) had higher IAAT/TAAT ratio than those with shorter disease and controls (0.35 ± 0.10 vs 0.28 ± 0.08, P = 0.0288 and 0.24 ± 0.04, P = 0.0009, respectively). In these patients, increased IAAT/height ratio was associated with complicated disease (P = 0.043, r = 0.573). No association was found between IAAT/TAAT ratio and actual disease activity or therapy.IAAT is increased in pediatric CD and correlates with disease duration. Assessment of IAAT accumulation may be considered in future MRI scores for inflammation and bowel damage in CD and during follow-up of different therapeutic interventions.