Background: Endothelial cell specific molecule-1 (ESM-1) or Endocan is a circulating dermatan sulphate proteoglycan secreted primarily by the vascular endothelium. Elevated levels of ESM-1 are observed in the plasma of patients during tumor progression and in inflammatory disorders like sepsis suggesting that it could be potential biomarker for endothelial activation or dysfunction. To date there have been no in vivo studies of ESM-1. In this study we investigated the in vivo functional role of ESM-1 by the targeted deletion of the gene in mice. Methods and Results: To determine the critical functions of ESM-1 in vivo, we generated a global ESM-1 knockout mouse by deletion of exon1 of the ESM-1 mouse gene. ESM-1 knockout mice were born at the normal Mendelian ratio but showed 50% perinatal mortality by postnatal day 3 (P3). Pathological analysis of mice that died at P2 revealed dilated atria engorged with blood and thrombi indicative of possible defect in cardiac contractility. Pulmonary and liver congestion were also observed in ESM-1 knockout mice. Furthermore, histopathological studies revealed structural abnormalities in atrioventricular valves (AV) with an ebstenoid tricuspid malformation and parachute mitral valve abnormality suggesting AV valve regurgitation in ESM-1 knockout mice. In contrast, the semilunar valves appeared normal. Fetal genes associated with cardiac stress response including atrial natriuretic peptide (Nppa), brain natriuretic pepetide (Nppb) and beta-myosin heavy chain (Myh7) were significantly up regulated in ESM1 knockout P2 hearts compared to controls. Conclusion: In conclusion, our findings demonstrate for the first time that targeted disruption of ESM-1 results in atrioventricular valve anomalies leading to cardiac dysfuction. Understanding the mechanisms and signaling networks through which ESM-1 regulates valve formation has implications in the field of congenital heart disease research