This case-control study was designed to investigate the prevalence of mutations in the prothrombin gene (20210A) and the factor V Leiden in unselected patients with venous thromboembolism (VTE). One hundred consecutive patients with objectively documented VTE (49 isolated pulmonary embolism, 45 pulmonary embolism + deep vein thrombosis, and 6 deep vein thrombosis) and 256 unmatched control subjects were included in the study. Seven percent of the 100 patients were found to be carriers of the prothrombin 20210A allele. This mutation was present in 2.3 % of the 256 controls (Odds ratio 3.13; 95% CI 1.02 - 9.57) (p=0.05). Twenty-four percent of the patients had the mutation of factor V Leiden while this mutation was present in 9.8 % of the 132 controls (OR:2.89; 95% CI 1.38 - 6.02) (p=0.006). Six patients were homozygous carriers of the factor V Leiden mutation and 4 patients shared both mutations. Patients with isolated pulmonary embolism (n=49) and patients with pulmonary embolism + deep vein thrombosis (n=45) showed similar prevalences for factor V Leiden mutation (24.4% and 17.8% respectively) and for prothrombin 20210A allele (8.1% and 4-4% respectively ). It was concluded that the 20210A allele of the prothrombin gene and factor V Leiden mutation are significantly higher in Turkish patients with VTE.