Adherent-invasive Escherichia coli (AIEC) has been reported as associated with the pathogenesis of inflammatory bowel disease (IBD). We aimed to investigate the characteristics of mucosa-associated E. coli and the clinical significance of AIEC in Korean IBD patients. E. coli strains were isolated from the mucosal tissues of 18 Crohn's disease (CD) patients, 24 ulcerative colitis (UC) patients, and 9 healthy controls (HC). Adhesion, invasion, and survival assays were performed to evaluate phenotypic features of E. coli isolates and to identify AIEC. The presence of virulence genes and cytokine expression were examined using PCR. In addition, data on IBD-related hospitalization were collected. A total of 59 E. coli strains were isolated (25 from CD, 27 from UC, and 7 from HC). The average levels of adhesion, invasion, and survival were higher in E. coli strains from IBD patients than those from HC (adhesion: 1.65 vs. 0.71, p = 0.046; invasion: 1.68 vs. 0.52, p = 0.039; survival: 519.55 vs. 47.55, p = 0.363). Prevalence of AIEC in HC, CD and UC patients was 22.2%, 38.9% and 37.5%, respectively. E. coli isolates from IBD patients had various virulence genes and were associated with increased expression of TNF-α and IL-17. IBD-related hospitalization within 3 years was 18.8% in patients with AIEC and 11.5% in patients without AIEC. E. coli strains from IBD patients showed high levels of adhesion, invasion, and survival. AIEC strains were identified in both CD and UC patients at a similar rate. AIEC may be associated with sustaining inflammation in the pre-existing inflammatory mucosa.