Crohn's disease treatment has improved significantly with the development of immunosuppressive and immunomodulatory agents, while surgery remains an important option in selected patients. However, a relative lag in diagnostics has become apparent with a growing need for the capacity to noninvasively and safely evaluate the tissue changes of Crohn's disease within the bowel wall and deeper tissues. We have noted marked technical improvements in magnetic resonance enterography (MRE) and in our understanding of the different facets of Crohn's disease that can be elucidated by optimized MRE, in contrast to other diagnostics. This review will provide an integrated understanding of MRE related to other available tests and recommendations for the optimal use of MRE for the clinical management of Crohn's disease. We will review the relative strengths and limitations of MRE as applied to clinical evaluation and therapeutic decisions, including the use of the unique capacity to delineate active inflammation and fibrosis in the submucosal and deeper enteric tissues, which is beyond the diagnostic reach of endoscopy and biopsy.