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In Crohn's disease, it is essential to distinguish between persistent damage and abnormalities that can heal with anti-inflammatory therapy.To assess magnetic resonance enterography (MRE) lesions that persist in patients in long-standing endoscopic remission, analyse their relationship with baseline characteristics, and determine their prognostic implications.We systematically reviewed pre- and post-treatment MRE findings in patients with Crohn's disease and severe inflammation (segmental CDEIS ≥ 7 or ulcers in at least one segment) who achieved endoscopic remission (CDEIS 2) after 1 year of treatment with TNF-inhibitors or autologous haematopoietic stem-cell transplantation. Logistic regression analysis was used to identify predictors of persistent abnormalities.Endoscopic remission was achieved in 73 intestinal segments in 28 patients (69% females; 9.95 years disease duration, 67.9% inflammatory phenotype; 39.3% ileal location). Creeping fat and intestinal wall fat deposits were unchanged on pre- and post-treatment MRE despite the endoscopic remission. Luminal strictures persisted in 6 out of the 8 segments with baseline strictures, and wall thickening in 23 out of the 72 of segments with thickening at baseline. Predictors of persistent mural thickening were pre-treatment wall thickness 5.9 mm (OR = 4.38, P = 0.027) and refractory disease prior to baseline (OR = 2.35, P = 0.001). Creeping fat was the only predictor for persistence of creeping fat (OR = 36.43, P 0.001). Persistence of strictures at MRE is associated with earlier recurrence (P = 0.014).Persistent MRE abnormalities are frequent in patients with Crohn's disease despite achieving endoscopic remission. Significant wall thickening, intestinal fat deposition, strictures, and creeping fat at baseline MRE are signs of established damage.