Background: Endoscopic mucosal healing is the current therapeutic target in Crohn's disease. However, transmural healing could lead to better outcomes. Aims: To assess whether transmural healing or magnetic resonance imaging (MRI) healing are better therapeutic targets than endoscopic mucosal healing to predict long-term improved outcome in Crohn's disease Methods: From our MRI database, we retrospectively identified all Crohn's disease patients who had MRI and colonoscopy within a 3-month interval (median interval = 17.5 days). Four groups were considered: endoscopic mucosal healing (no ulceration or aphthoid erosion), MRI healing (no MRI signs of inflammation and no complication), transmural healing (combination of endoscopic and MRI healing) or no healing. Outcomes were time to surgery, bowel damage progression, hospitalisation, major outcomes (one of the three previous endpoints) and Crohn's disease-related drug discontinuation. Results were expressed in multivariable analyses adjusted on potential confounders (hazard ratio (HR) [95% confidence interval]). Results: Among 154 patients with Crohn's disease, 51.9% (80/154), 10.4% (16/154), 19.5% (30/154) and 18.2% (28/154) achieved no healing, endoscopic mucosal healing, MRI healing and transmural healing, respectively. Transmural healing (HR = 0.05 [0.00-0.40], P = 0.002) and MRI healing (HR = 0.09 [0.00-0.47], P = 0.005) were associated with lower risk of bowel damage progression than endoscopic mucosal healing. In addition, achieving transmural healing or MRI healing reduced the risk of experiencing major outcomes compared to endoscopic mucosal healing (HR = 0.28 [0.00-0.74], P = 0.01). Patients with transmural healing also had a decreased risk of relapse-related drug discontinuation (HR = 0.35 [0.13-0.95], P = 0.039) compared to those with endoscopic mucosal healing. Conclusion: Transmural healing and MRI healing are associated with lower risk of bowel damage progression than endoscopic mucosal healing and could be considered as better therapeutic targets in Crohn's disease.