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Mucosal healing (MH) is currently accepted as one of the best treatment targets in Crohn's disease. However, even in patients with sustained MH, residual bowel wall inflammation can still be detected by cross-sectional imaging. The long-term benefits of obtaining transmural healing (TH) have not been previously assessed.We performed an observational study including 214 patients with Crohn's disease with a magnetic resonance enterography (MRE) and colonoscopy performed within a 6-month interval. Patients were classified as having TH (inactive MRE and colonoscopy), MH (active MRE with inactive colonoscopy), or no healing (active colonoscopy). Need for surgery, hospital admission, and therapy escalation were evaluated at 12 months of follow-up.Patients with TH presented lower rates of hospital admission, therapy escalation, and surgery than patients with MH or no healing. In logistic regression analysis, endoscopic remission (odds ratio 0.331 95% confidence interval [0.178–0.614], P < 0.001) and MRE remission (odds ratio 0.270 95% confidence interval [0.130–0.564], P < 0.001) were independently associated with a lower likelihood of reaching any unfavorable outcome.TH is associated with improved long-term outcomes in Crohn's disease and may be a more suitable target than MH.