Background Intestinal Behçet's disease (BD) is a chronic inflammatory bowel disease, as are Crohn's disease (CD) and ulcerative colitis (UC). But unlike CD and UC, serologic markers for intestinal BD are not well known. Recently, antia-enolase antibody (AAEA) has been detected in sera from BD patients. Aims The aim of this study was to evaluate the prevalence of AAEA in intestinal BD and its clinical correlations. Methods The study sample included 80 patients with intestinal BD and 23 healthy controls. IgM AAEA was detected by ELISA. The positivity of IgM AAEA was defined as an optical density greater than three standard deviations above the mean of the control sera. Other parameters, such as demographic information, subtype of BD, colonoscopic findings, disease severity and treatment modality, were analyzed retrospectively. Results The prevalence of IgM AAEA was 67.5% in intestinal BD and 0% in the control group. The positivity rate of IgM AAEA was higher in complete or incomplete BD than in suspected BD (77.5% vs. 51.6%, P = 0.016). The mean HBI score was higher in antibody positive patients than in antibody negative patients (5.60 vs. 4.61, P = 0.003). The cumulative probability of steroid use for aggravation of intestinal and extra-intestinal symptoms was higher in antibody positive patients than in antibody negative patients (P = 0.012). The number of patients with systemic involvement was higher in the AAEA positive group than in the negative group. Conclusions Monitoring IgM AAEA may be helpful for diagnosis of intestinal BD and could be used to predict clinical course and disease severity.