Data regarding early atherosclerosis and inflammatory bowel disease are limited and conflicting results are present. The purpose of this study was to evaluate serological and sonographical evidence of subclinical vascular involvement in patients with inflammatory bowel disease. Thirty-nine patients with inflammatory bowel disease (20 Crohn's disease, and 19 ulcerative colitis patients) and 31 healthy controls were consecutively enrolled in the study. Flow mediated dilatation of the brachial artery and intima media thickness assessments of the common carotid artery were measured sonographically. Soluble CD40 ligand levels were evaluated. Crohn's disease activity index and modified Truelove-Witt's criteria were also noted. Age, sex distribution, serum lipids, smoking status, and intima media thickness of the common carotid artery were similar between the inflammatory bowel disease patients and controls (p > 0.05). However, both endothelium dependent and independent flow mediated dilatation values were significantly impaired in the inflammatory bowel disease group compared with healthy controls (p < 0.05). Erythrocyte sedimentation rate, C-reactive protein and soluble CD40 ligand values were significantly increased in inflammatory bowel disease patients compared with controls (p < 0.05), and soluble CD40 ligand was negatively correlated with flow mediated dilatation (r = -0.3, p < 0.05). Flow mediated dilatation was significantly predicted from the concentrations of C-reactive protein and soluble CD40 ligand. Functional atherosclerosis is present in inflammatory bowel disease before early structural changes occur in vasculature. Higher sCD40L may indicate worse vascular outcome for IBD.