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Objective: To study the frequency of Factor V Leiden (FVL), prothrombin gene mutation G20210A and methylenetetrahydrofolate reductase C677T in patients with acute pulmonary embolism (PE); and to investigate whether these factors are more frequent in patients who have no obvious risk factors for venous thrombo-embolism compared to those with obvious risk factors., Methods: A case-control study conducted at Jordan University Hospital, Amman, Jordan during the period 2005-2007. Compared 92 patients with acute PE to 99 normal subjects. All subjects were investigated for the 3 genetically related thrombophilic factors., Results: The frequency of these factors in patients were 22/92 (23.9%) FVL, 3/92 (3.3%) Factor II (FII) and 48/92 (52.2%) methylenetetrahydrofolate reductase (MTHFR). In the control group, FVL was 12/99 (12.1%), FII 0/99 (0%), and 53/99 (53.5%) MTHFR. There was a statistically significant difference between patients and controls for FVL (p=0.03), but no statistical significance for FII (p=0.10) and MTHFR (p=0.85). In patients with no obvious risk factors, the frequency of these factors were 8/29 (27.6%) FVL, 2/29 (6.9%) FII, and 14/29 (48.3%) for MTHFR compared to patients with obvious risk factors 14/63 (22.2%) for FVL, 1/63 (1.6%) FII, and 33/63 (52.3%) MTHFR., Conclusion: The FVL is statistically more frequent in patients with PE compared to the control group, and the frequency of FVL, FII, and MTHFR is not significantly higher in patients with acute PE who have no obvious risk factors compared to those with obvious risk factors.