Prosthetic valve thrombosis (PVT) is a critical and life-threatening condition, driven by multifactorial etiologies including genetic predispositions. The study was designed as a single-center retrospective manner. Echocardiographic features and genetic test including Factor II Prothrombin G20210A, Factor V Leiden G1691A, Factor V R2 A4070G, ApoB-100 G10708A, ApoE C112R, ApoE R158C, MTHFR C677T, MTHFR A1298C, Factor XIII G103T (V34L), Beta fibrinogen G-455A, PAI-1 4G/5G, and HPA-1 (GPIIIa) T196C genotyping variations were assessed. We performed genetic tests in 175 patients with PVT [biologically women (n=124, 70.9%) with a mean age of 49.8 ± 13.1 years], and in 101 patients [biologically women (n=57, 56.4%) with a mean age of 54.7 ± 13.6 years] without thrombus formation. The thrombosis group was significantly younger compared to controls (p=0.004). The percentage of patients with mechanical aortic valves was significantly lower in the thrombosis group compared to controls (22.3 vs 34.7%, p=0.025). A significant difference was observed between the thrombosis and control groups regarding the genotype ratios of Factor II/Prothrombin (G20210A) (heterozygous, 6.8 vs 1%, p =0.043) and HPA-1 GPIIIa (T196C) (homozygous mutant, 7.8 vs, 0%, p=0.034) In addition, there was a significant association of heterozygous MTHFR (A1298C) variation with obstructive thrombosis compared to non-obstructive thrombosis (46.9 vs 29.2%, p=0.046). In conclusion, this is the first study to report a potential association between genetic variants including HPA-1 GPIIIa (T196C), Factor II/Prothrombin (G20210A), MTHFR (A1298C) and PVT, necessitating extensive further research and additional clinical consideration.