Behçet disease (BD), enterocolic lymphocytic phlebitis (ELP), idiopathic myointimal hyperplasia of mesenteric veins (IMHMV), and mesenteric arteriovenous dysplasia/vasculopathy (MAVD/V) are rare vascular diseases (VDs) that cause bowel ischaemia, often presenting with a histological pattern resembling chronic enteritis, leading to diagnostic confusion with Crohn disease (CD). In this retrospective study, we compared the clinical and pathological characteristics of these VDs with those of CD. The study cohort comprised 13 patients misdiagnosed with CD but later identified as having VDs, including five, three, two, and three patients with BD, ELP, IMHMV, and MAVD/V, respectively. Moreover, 15 patients diagnosed with CD served as the control group. Data on disease history, patient demographics, symptoms and signs, endoscopic findings, clinical diagnosis, and follow-up status were collected, and the histological features of VDs were compared with those of CD. Despite substantial overlap in clinical and pathological characteristics between VDs and CD, several histological features were helpful in differentiating the two conditions. Intestinal stenosis, multisegmental disease, transmural inflammation, inflammatory polyps, submucosal lymphangiectasia, intramural abscesses, and epithelioid granulomas were significantly more frequent in patients with CD (p<0.001). In contrast, toxic ischaemic changes and vascular lesions were significantly more frequent in patients with VDs (p<0.001). The location of diseased vessels varied widely in patients with VDs, whereas vascular changes were limited to areas with more severe inflammation in those with CD. Furthermore, inflammatory cells within diseased vessels exhibited a polarised distribution in cases of CD, manifesting in two distinct patterns: pattern 1, where the inflammatory cells are densely populated in the outer layer of the vessel wall and sparsely populated in the inner layer; pattern 2, where the inflammatory cells are densely populated on the side with the ulcer and sparsely populated on the opposite side. Vascular occlusion, which was observed in all patients with VDs, was rare in those with CD. In summary, VDs and CD can be distinguished through careful histological analysis, particularly focusing on characteristics of vascular changes, in combination with medical history.