BackgroundCurrently available tools for noninvasive motility quantification of the small intestine are limited to dynamic 2D MRI scans, which are limited in their ability to differentiate between types of intestinal motility.PurposeTo develop a method for quantification and characterization of small intestinal motility in 3D, capable of differentiating motile, non‐motile and peristaltic motion patterns.Study TypeProspective.SubjectsFourteen healthy volunteers (127 small intestinal segments) and 10 patients with Crohn's disease (87 small intestinal segments).Field Strength/Sequence3.0 T, 3D balanced fast field echo sequence, 1 volume per second.AssessmentUsing deformable image registration between subsequent volumes, the local velocity within the intestinal lumen was quantified. Average velocity and average absolute velocity along intestinal segments were used with linear classifiers to differentiate motile from non‐motile intestines, as well as erratic motility from peristalsis. The mean absolute velocity of small intestinal content was compared between healthy volunteers and Crohn's disease patients, and the discriminative power of the proposed motility metrics for detecting motility and peristalsis was determined. The consensus of two observers was used as referenced standard.Statistical TestsStudent's t‐test to assess differences between groups; area under the receiver operating characteristic curve (AUC) to assess discriminative ability. P < 0.001 was considered significant.ResultsA significant difference in the absolute velocity of intestinal content between Crohn's patients and healthy volunteers was observed (median [IQR] 1.06 [0.61, 1.56] mm/s vs. 1.84 [1.37, 2.43] mm/s), which was consistent with manual reference annotations of motile activity. The proposed method had a strong discriminative performance for detecting non‐motile intestines (AUC 0.97) and discernible peristalsis (AUC 0.81).Data ConclusionAnalysis of 3D cine‐MRI using centerline‐aware motion estimation has the potential to allow noninvasive characterization of small intestinal motility and peristaltic motion in 3D.Evidence Level3Technical EfficacyStage 2