Thrombophilia includes multiple inherited and acquired risk factors that determine a shift in the balance of procoagulant and anticoagulant factors promoting hypercoagulability, which is associated with an increased risk of venous thromboembolism (VTE). VTE is characterized by more common clinical manifestations, such as deep vein thrombosis of the lower limbs or pulmonary embolism, and less common clinical manifestations affecting cerebral, splanchnic, upper limbs, and retinal veins. The role of inherited thrombophilia in the pathogenesis of VTE at unusual sites is better established in cerebral vein thrombosis, but its role is less clear in splanchnic, upper limbs, and retinal vein thrombosis, in which acquired risk factors such as malignancy, central venous catheters, or systemic diseases also are frequently involved. The complex interactions between different inherited and acquired thrombophilic risk factors and their relationship with endothelium may be considered the pathophysiologic key of underlying phenotypic manifestations of thrombosis. The understanding of these mechanisms might facilitate diagnosis with appropriate investigations and improve therapeutic decision making.