The mechanisms of thrombosis in antiphospholipid syndrome (APS) are highly heterogeneous and multifactorial, and some genetic factors may be involved in its pathophysiology. The genetic variants of representative antigen, beta 2-glycoprotein I (beta 2GPI), have been known, and valine/leucine247 polymorphism is a genetic risk for having anti beta 2GPI antibodies and APS. Congenital beta 2GPI deficiency did not correlate with thrombophilia, thus its responsible gene (beta 2GPI-Sapporo) was not a risk for thrombosis. Many other thrombosis-related genetic factors have been investigated in APS, but no additional risk for thrombosis has been indicated in patients with antiphospholipid antibodies.