Achieving deep remission, encompassing clinical, endoscopic, and biological remission, is the goal in managing Crohn's disease (CD). The role of histological remission remains unclear. This study aimed to examine the impact of histological inflammation on clinical relapse risk in CD and explore the relationship between histology, endoscopic scores, and biomarkers. Patients from the prospective STORI cohort underwent ileocolonoscopy with CDEIS calculation and 2 biopsies from the most inflamed or previously inflamed areas. Histological scores (Robarts, Geboes, modified Geboes, Nancy, and IBD-DCA) were determined by two independent pathologists in a central reading process. Histological remission was defined by specific score thresholds. Clinical relapse, defined by CDAI >250 or a CDAI increase of 70 points over two weeks, was monitored for at least one year. Out of 115 patients included in STORI, 160 biopsies (44 ileal and 116 colonic) from 76 patients were analyzed. Histological remission rates were 46% (Nancy), 55% (Robarts), 61% (Geboes), and 41% (IBD-DCA). During follow-up, 35 patients (46%) experienced a clinical relapse: 37% with histological remission and 56% without, based on the Nancy score. Among the mucosal healing (MH) subgroup (45 patients), 34% with histological remission and 44% without relapsed (p=0.18). Histological scores did not predict clinical relapse. Only faecal calprotectin (FC) was a significant predictor in multivariate analysis (p=0.029). Despite correlations with endoscopy and biomarkers, histological scores did not predict clinical relapse in CD patients in remission. Thus, these scores are not recommended for clinical practice to assess relapse risk in CD.