Several inherited polymorphisms are associated with the risk of venous thrombosis, including mutation at codon 506 of the factor V gene and mutation at position 20210 of the prothrombin gene. The aim of this study was to determine the frequency of factor II G20210A and factor V Leiden mutations in Algerian patients with venous thromboembolism disease. In this study, genotyping for factor V Leiden and factor II G20210A mutations was performed in 40 patients with venous thrombosis by the GeneXpert Dx. According to the results of the study, factor V Leiden was detected in 5 patients (12.5%) and factor II G20210A was detected in only one patient (2.5%). Both mutations were found in heterozygous form and no patient was double heterozygous. In conclusion, the prevalence of factor V Leiden mutation was high among Algerian patients with venous thromboembolism disease however, further studies are needed in order to estimate the true prevalence of factor II G20210A and factor V Leiden mutations within this population as well as to verify where exactly they have occurred first and how they were carried to other parts of the world. Furthermore, it is hoped that new approaches namely the GWAS could be adopted towards the identification of new genetic risk factors within the Algerian population.