Early recognition of Crohn's disease with initiation of disease-modifying therapy has emerged as a prominent inflammatory bowel disease management strategy. Clinical practice and trials have often focused on patient symptoms, and more recently, serologic tests, stool inflammatory markers, and/or endoscopic inflammatory features for study entry criteria, treatment targets, disease activity monitoring, and to assess therapeutic response. Unfortunately, patient symptoms do not correlate well with biological disease activity, and endoscopy potentially misses or underestimates disease extent and severity in small bowel Crohn's disease. Computed tomography enterography and magnetic resonance enterography (MRE) are potential tools to identify and quantify transmural structural damage and disease activity in the small bowel. In this review, we discuss the role of computed tomography enterography and MRE in disease management algorithms in clinical practice. We also compare the currently developed MRE-based scoring systems, their strengths and pitfalls, as well as the role for MRE in clinical trials for Crohn's disease.