Background: Thrombophilia, a predisposition to develop blood clots, is very common and can have serious sequelae. Aim: This study aimed to determine the prevalence of three thrombophilia-related genetic variants-factor V Leiden (FVL), prothrombin (F2) G20210A, and MTHFR C677T-in the Qatari population and their associations with self-reported thrombosis. Methods: We analysed samples from 408 Qatari participants [304 controls and 104 with self-reported thrombosis (deep vein thrombosis, pulmonary embolus, or ischaemic stroke)] from the Qatar Biobank. FVL (rs6025), F2 (rs1799963), and MTHFR (rs1801133) variants were genotyped using TaqMan assays. Results: Participants with self-reported thrombosis were older and more likely to be female. FVL A allele carriage (GA + AA vs. GG) was significantly higher in thrombosis cases (OR 3.6, p = 0.0002). In addition, individuals carrying FVL AA and GA genotypes had a lower mean platelet volume on average than those with the GG genotype (p = 0.03). MTHFR C677T did not show a similar association, and the F2 G20210A variant was too rare for analysis. Conclusions: There were significant differences in FVL A allele carriage between individuals with a history of thrombosis and the control group. Future research should explore the complex interplay between genetics and environment in thrombosis risk within this population.