Background: Factor V leiden and the -G20210A variant of prothrombin gene are associated to a higher risk of deep venous thrombosis. Aim: To assess the frequency of factor V Leiden (G1691A) and prothrombin -G20210A alleles in patients with deep venous thrombosis (DVT) and in the general population from Spain. Material and methods: Factor V Leiden (g1691a) and prothrombin-g20210a alleles were genotyped in 493 individuals from the Spanish general populations and in 131 patients with DVT. The presence of DVT was confirmed by phlebography. Allelic frequencies and the DVT risk associated with these variants were estimated. Results: Allelic frequencies for the factor V Leiden (G1691A) allele were 0.019 in patients with DVT and 0.010 in the general population (p=0.235). The frequencies for the prothrombin-G20210A allele were 0.027 and 0.026 (p=0.975). After adjustment for age and gender, the odds ratio for DVT, associated with the presence of G1691A allele was 2.41, but not statistically significant (95% confidence intervals 0.63-9.19). Conclusions: Prothrombin-G20210A allele was more prevelant than factor V Leiden (G1691A) allele in the Spanish population. However, the magnitude of the association between the G20210A and DVT risk is very low. On the contrary, the G1691A allele is associated by itself with a two fold increase in DVT risk in this population although without reaching statistical significance due to its low frequency