Magnetic resonance enterography (MRE) is an accurate examination for assessing activity in Crohn's disease (CD). Various MRE indices have been developed for that purpose, but have not been directly compared. The aim of the study was to compare the diagnostic accuracy of three MRE indices for detecting and grading disease activity in CD, using endoscopy as gold standard. MRE and ileocolonoscopies performed within 1 month in 43 patients with CD were analyzed. The magnetic resonance index of activity (MaRIA), Clermont, and London indices for each colonic segment and the terminal ileum were calculated. Simplified endoscopy score for CD (SES-CD) was considered the gold standard. Two hundred and twenty-four intestinal segments were included in the analysis. According to the established cut-off points for detecting active disease using MaRIA, Clermont, and London indices, the sensitivity of each index was 0.88, 0.89, and 0.71, and the specificity was 0.97, 0.78, and 0.99, respectively. The sensitivity for detecting ulcerations was 0.90 and 0.83 for the MaRIA and Clermont indices, respectively, with a specificity of 0.91 and 0.89. The AUROC curve for the MaRIA, Clermont, and London indices for detecting active disease was 0.92, 0.84, and 0.85, and for detecting ulcerations was 0.90 for the MaRIA, and 0.86 for Clermont index. The three MRE-based indices evaluated in the current study have high diagnostic accuracy for assessment of disease activity. The MaRIA index has the best operational characteristics for detecting not only disease activity but also for grading severity, which supports its use in clinical studies and clinical practice.