Introduction. Antiphospholipid syndrome (APS) is an autoimmune thrombophilia in which patients with clinical criteria for recurrent arterial and venous thrombosis and/or pregnancy failure show positive laboratory results for the presence of antiphospholipid antibodies (aPL). The genetic predisposition to non-infectious endocarditis (NIE) in patients with APS remains a complex and poorly understood problem. Aim. Revealing of possible associations between polymorphisms of candidate genes and non-infectious endocarditis in patients with APS, as well as the development of possible thromboembolic complications. Materials and methods. The study involved 35 patients aged 43.0 ± 13.9 years. At the same time, the main signs characterizing NIE in APS were negative blood culture, normothermia, and the absence of obvious echoscopic signs of infection (thickening and induration calcification of the valve leaflets, minimal regurgitation). Polymorphisms of 18 genes were studied as possible molecular genetic markers for the development and/or protection of NIE in 35 patients with APS: the primary disorder was diagnosed in 15 patients (18.5%), secondary – in 20 patients with autoimmune patho¬logy (24.7%). Results. For the first time, for polymorphisms rs6025 (1691 G>A) of the F5 gene, 4а/4b of the NOS3 gene, rs1800795 of the IL6 gene, rs1805087 (2756 A>G) of the MTR gene, a significant association with the development of vegetations on the valvular heart apparatus in APS was revealed. Two polymorphisms, rs1126643 (807 C>T) of the ITGA2 gene and rs1799889 (-675 5G>4G) of the PAI1 gene (SERPINE1), were found to be associated with thromboembolic complications (acute cerebrovascular accident) in NIE. Conclusion. It is reasonable to perform genotyping of some single nucleotide polymorphisms in patients with APS.