Thalassemia major patients have increased risk for thromboembolic complications because of the chronic hypercoagulable state. The question arising from this is whether thromboembolic complications are the result of genetic polymorphisms of prothrombotic factors. Here, we studied factor V 1691 G-A (FVL), factor II polymorphism (G20210A), methyltetrahydrofol ate reductase mutation (MTHFR, C677T), and endothelial cell protein C receptor (EPCR) deletion polymorphism and their relationship with thromboembolic complications. We found significant decrements of protein C and protein S and a slight increased prevalence of congenital thrombophilic mutations when compared with controls. Although 5 of the patients bad high soluble EPCR (sEPCR) levels, no significant change was found in sEPCR values between patients and controls.