Evaluation of small bowel motility from two-dimensional dynamic MRI is of increasing interest for the assessment of segmental diseases such as Crohn's disease. We propose to use nonrigid image registration for automated motility analysis. Registration is particularly difficult when localized intensity changes occur (e.g., due to intraluminal flow or through-plane motion). Therefore, displacements were extracted using a joint registration and modeling of intensity changes. Results were analyzed in 10 patients with known or suspected Crohn's disease. Bowel wall displacements were assessed by tracking bowel cross-sectional markers over time. Automated tracking with the proposed technique was in good agreement with manual tracking (similar bias, improved standard deviations). The ability to quantify different grades of bowel motility was investigated by comparing direct motion measures (i.e., changes in bowel cross-sectional diameter or area) and various parametric maps, e.g., based on the Jacobian of the measured displacements with expert grading. Among these measures, the standard deviation over time of the Jacobian was the best at predicting grades from 1 (moving normally) to 4 (not moving at all) in 50 bowel regions with normal and pathologically reduced motility, yielding 93% correct classification with a 1-class tolerance (i.e., same score as the expert ± 1). Magn Reson Med, 2012. © 2012 Wiley Periodicals, Inc.