Atherosclerosis is a disease of blood vessels which is caused by inherited and acquired factors and leads to different complications in the body including blood clot formation, a serious condition that can threat human life. This study aims to measure the prevalence of thrombophilia gene mutations; Factor V Leiden (FVL, G1691A) and F-II (G20210A) in Jordanian patients with atherosclerosis. Using real-time PCR, the prevalence of heterozygous and homozygous variants of FVL (G1691A) were 11.32 and 1.87% respectively. In F-II (G20210), the prevalence was 1.87 and 0.31% for heterozygous and homozygous variants, respectively. Comparing mutants' frequencies between patients with atherosclerosis and healthy people (control) showed no significant difference suggesting no relation of these mutants and thrombus formation in atherosclerotic patients, however, among patients' group there was a significant difference in the prevalence of FVL (G1691A) variants between male and female populations and insignificant difference for F-II (G20210). In conclusion, the results of this study showed no relation of inherited F-V and F-II gene mutations in blood clot formation in atherosclerotic patients, suggestion that blood clot formation is related only to environmental factors belong to the nature of atherosclerotic plaque which trigger platelets and clotting proteins activation.