Background Magnetic resonance imaging (MRI) can assess disease activity and severity in Crohn’s disease (CD). Three-Tesla magnetic resonance (3T) increases signal-to-noise ratio (SNR) and reduces time of image acquisition (IAT). Whether 3T increases the accuracy of MRI in CD compared to 1.5T is unknown. Aim We aimed to compare prospectively the accuracy of 3 and 1.5T in ileo-colonic CD patients. Methods Twenty-six patients with ileo-colonic CD underwent 1.5 and 3T MR enterography at the same time. Ileocolonoscopy was the reference standard for luminal disease. Sensitivity, specificity and accuracy of MRI in evaluating six signs of active and complicated disease (localization, thickening, enhancement, strictures, entero-enteric fistulas, and ulcers) were calculated for both techniques. Results Three-Tesla resulted as sensitive, specific, and accurate as 1.5T in detecting disease location (accuracy 0.93 vs. 0.86), bowel wall thickening and enhancement (accuracy 0.92 vs. 0.80 for both parameters), strictures (accuracy 0.90 vs. 0.80) and entero-enteric fistulas (accuracy 0.92 vs. 0.92). 3T was superior to 1.5T in detecting ulcers (0.76 vs. 0.42, P < 0.05). SNR resulted higher in 3T, and IAT resulted shorter than 1.5. Conclusions We found that 3T is equally accurate as 1.5T in evaluating ileo-colonic CD. Because of superiority in detecting mucosal ulcers, 3T should be preferred in patients with ileo-colonic CD.