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Recurrent non-organic abdominal pain is the most commonly diagnosed medical problem in children. However, excluding small bowel disease remains a challenge. We evaluated our exclusion criteria for organic small intestinal diseases in pediatric patients with recurrent non-organic abdominal pain using cinematic magnetic resonance (cine-MR) enterography.The non-intestinal organic (non-IO) group as classified by the Rome III criteria system and the intestinal organic (IO) group consisted of 81 and 19 patients, with 35 and 12 male and 46 and 7 female patients with an age range of 5–18 and 4–15 years (average 10.5 and 10.5 years), respectively. Cine-MR enterography was performed by dynamically balanced first-field-echo imaging with thick-slice water-selective excitation without breath holding. In our original small intestinal motility test, cine-MR enterography was taken at three different times (fasting state [P1], immediately after [P2] and 30 min after [P3] drinking liquid material), with images taken sequentially for 5 min at each time-point to evaluate the motion of water in the gastrointestinal tract. Positive findings for organic intestinal problems were concluded when persistent visible intestinal loops appeared in both the P1 and P2 phases.Cine-MR enterography showed 6/81 (7.4%) and 18/19 (94.7%) (P < 0.01) positive cases of organic intestinal problems in the non-IO and IO groups, respectively. Positive and negative predictive values of this examination were 78.3% and 97.4%, respectively.The unique capabilities of cine-MR enterography technology in this clinical setting render it an important additional diagnostic tool when specific disease management issues must be addressed.