Thrombosis secondary to Glenn anastomosis in Ebstein’s anomaly has been reported very rarely, treatment depends on presenting symptoms and risk factors. In this article we presented the case of 63-year-old woman with Ebstein’s anomaly (implantation of biological tricuspid valve ,Glenn procedure, closure of patent foramen ovale and implantation of DDD type pacemaker with epicardial electrodes) who complained on neck discomfort while tilting head forward .Eventually in whom thrombosis within Glenn anastomosis was diagnosed by angio-CT scan. JRCD 2015; 2 (3): 89–91