BACKGROUND: Cross-sectional imaging techniques as magnetic resonance enterography (MRE) may offer additional information on transmural inflammation, stricturing and fistulising complications in Crohn's disease (CD). The purpose of our study was to evaluate the diagnostic accuracy of Magnetic Resonance Imaging (MRI) combined with Diffusion-weighted Imaging (DWI) and MRE for determination of inflammation in small bowel CD. METHODS: MR imaging examination was performed with a GE Signa EXCITE 3.0 T MRI scanner. The optimal b value in DWI with a learning cohort of patients was determined. The diagnostic accuracy for active lesions and disease activity were accessed by MRE combined with DWI. RESULTS: The b value 800 s/mm(2) group showed the highest diagnostic sensitivity (74.19%) for diagnostic assessment of active Crohn's lesions on DWI. MRE combined with DWI showed the highest sensitivity (93.55%), specificity (89.47%) and diagnostic accuracy (92%) compared with MRE or DWI alone. The segmental MR score (MR-score-S) showed a significantly positive correlation with the Capsule Endoscopy Crohn's Disease Activity Index Score (CECDAI-S) (r = 0.717, p < 0.01). The total MR score (MR-score-T) showed significant association with C-reactive protein (CRP) (r = 0.445, p = 0.019) and erythrocyte sedimentation rate (ESR) (r = 0.688, p < 0.01). CONCLUSIONS: MRE combined with DWI improves the diagnostic accuracy for active lesions and correlates the endoscopic disease activity. MRE with DWI could represent a non-invasive tool in assessing active inflammation in CD.