Objective: To compare multidetector-row computed tomographic (MDCT) enterography with magnetic resonance (MR) enterography performed upon acute exacerbation of Crohn's disease. Subjects and Methods: Fifty-seven patients (mean age 33.5) with proven Crohn's disease and symptoms suggesting acute exacerbation were prospectively included. After oral administration of 1-2 liters of 5% methylcellulose, MDCT and MR enterography were performed on each patient (mean delay <24 h). Three radiologists blindly and independently evaluated each examination for technical quality and in terms of 8 pathological features of Crohn's disease. Observers' agreement, sensitivity and specificity resulted from comparison with the reference standard [surgery (n = 24), endoscopy (n = 17) and long-term follow-up (n = 16)]. Results: MDCT enterography demonstrated fewer artifacts than MR enterography (p < 0.0001). In 48 MDCT/MR enterography examinations, active disease was demonstrated: abscesses (n = 11), fistulas (n = 13), stenoses (n = 23) and/or intestinal inflammation (n = 38). Observers' agreement (range 0.56-0.87) was not significantly different between MDCT and MR enterography, neither in terms of sensitivity (range 58-95%) nor specificity (range 67-100%) for each of the 8 pathological features. Conclusion: Statistically, MR enterography is of similar diagnostic value as MDCT enterography for acute complications of Crohn's disease. Since the typical Crohn's disease patient is young and will very likely undergo life-long imaging, and given concerns about radiation exposure with MDCT, MR enterography should be the preferred modality.