Crohn's disease leads to complications in the majority of patients on the long term. Strictures, fistulas and abscesses usually involve the bowel wall or extra-intestinal compartments, and conventional diagnostic tools, such as colonoscopy or barium studies, are not able to assess them. Magnetic resonance imaging has been proven to be accurate in detecting activity, severity and complications of Crohn's disease. Because of its reproducibility and safety, it can be considered the first-choice technique to complete Crohn's disease staging, and to monitor disease evolution. Recently, the concept of bowel damage has risen into the field of inflammatory bowel diseases. It has been shown that bowel damage induced by the disease can impact on patients' life, beyond intestinal symptoms. Data coming from rheumatology suggest that blockade of organ damage should be achieved independently from disease-related symptoms, and that a "damage driven" approach should be preferred than a "symptom-driven" one. This review of the literature aims to investigate the role of magnetic resonance imaging in assessing disease complications, which cause organ damage, and to explore future perspective in order to develop new therapeutical strategies and new tailored therapies, based on the prevention of intestinal damage.