The effect of thrombophilic mutations in the development of thrombosis in patients with antiphospholipid syndrome (APS) has been extensively investigated. Factor XIII (FXIII) Val34Leu polymorphism is a newly described polymorphism which is located in the three amino acids away from the thrombin activation site of the FXIII-A subunit. It has been reported that the Leu allele decreases the risk of both arterial and venous thrombosis. In the present study, we examined the association between the FXIII Val34Leu polymorphism and the development of thrombosis in patients with A-PS. Sixty A-PS patients with arterial and venous thrombosis, 22 antiphospholipid antibody (aPLA) positive patients with first trimester abortus and/or thrombocytopenia, 126 healthy controls, and 60 healthy subjects who were age- and sex-matched with thrombotic APS group were included into the study. FXIII Leu allele frequencies in the APS patients with thrombosis, aPLA-positive patients without thrombosis, healthy controls, and matched controls were 13.3, 16, 19.5, and 18.3%, respectively. When we compared Leu allele frequencies between APS patients with thrombosis and aPLA-positive patients without thrombosis, healthy controls or matched controls, we could not find any difference (chi(2), P = 0.43, and P = 0.09, P = 0.67, respectively). Our results showed that the FXIII Leu allele has no protective effect in the development of thrombosis in APS.