BACKGROUND: The clinical relevance and underlying mechanism of isolated anastomotic ulcers (IAUs) following ileocolic resection (ICR) in patients with Crohn's disease (CD) are poorly understood. This study aimed to assess the postoperative recurrence (POR) risk and the mucosa-associated microbiome composition in CD patients with or without IAUs among those with a healthy neo-terminal ileum (TI). METHODS: CD patients who underwent ICR and without any ulcerations in the neo-TI (SES-CD </=2) at first postoperative ileocolonoscopy were identified from an ongoing prospective multicenter study. The primary study outcome was time to POR measured from the first postoperative ileocolonoscopy. Cox proportional hazard models were used to assess the association of IAUs with time to POR. The mucosa-associated microbiome at first ileocolonoscopy was assessed by sequencing the 16S rRNA gene using biopsies taken from both sides of the anastomosis. RESULTS: Sixty patients were included, of whom 27 patients had IAUs (45.0%) at first ileocolonoscopy. Median time to first postoperative ileocolonoscopy was 6.5 months (interquartile range [IQR] 5.3-8.1). During a median follow-up duration of 3.0 years (IQR 1.4-5.5) after first postoperative ileocolonoscopy, POR was observed in 53.3%. After adjustment for clinical risk factors, IAUs were independently associated with POR (adjusted hazard ratios 5.4; 95% CI 2.4-12.4; P < .001). At the ileal and colonic side of the anastomosis, a significantly higher abundance of Klebsiella was associated with IAUs (q < 0.05). CONCLUSIONS: IAUs in CD patients with otherwise healthy neo-TI at first postoperative ileocolonoscopy are associated with long-term POR. In addition, a differential mucosa-associated microbiome composition was observed in patients with IAUs, specifically the proteobacteria Klebsiella, suggesting that putative taxa are related to these lesions. Further validation studies in larger cohorts, along with mechanistic studies, are still required.