In MR enterography, diffusion-weighted MRI (DW-MRI) is commonly used to evaluate Crohn’s disease (CD). Echo-planar imaging (EPI) used in DW-MRI suffers from geometric distortion due to time-varying susceptibility field changes in the bowel. Hence, we implemented a DW-MRI sequence using a dual-echo EPI with opposing encoding polarities. Thus, the distortion field can be estimated dynamically and corrected retrospectively. The proposed method was evaluated in DW-MRI data acquired on suspected CD patients by visually and quantitatively assessing distortion corrected volumes based on anatomical similarity with T2-HASTE and uncertainty of estimated diffusion parameters of the intravoxel incoherent motion model.