Gastrointestinal tract conditions, including inflammatory bowel diseases (IBDs) such as ulcerative colitis (UC) and Crohn’s disease, have been linked to adhesive invasive Escherichia coli (AIEC) pathotypes, with comparable pathogenic properties, although the incidence of AIEC with UC and CD is generally undetermined. While a significant advance has been made in understanding the pathogenic processes of AIEC since it was first characterized a decade ago, the molecular basis that determines the phenotypic features of AIEC pathotypes is still unknown. This article reviews studies that examine the prevalence of E. coli in patients with IBD and discusses its pathophysiological role.