One hundred beta-thalassemia major (beta-TM) patients and 100 individuals as control were included. Factor V Leiden and prothrombin G20210A and methylenetetrahydrofolate reductase (MTHFR) gene mutations were genotyped by PCR and allele-specific restriction enzyme techniques. The prevalence of factor V Leiden G1691A, MTHFR C677T and prothrombin G20210A in patients was insignificantly higher than controls. Patients with beta-TM have insignificantly higher frequencies of mutant A allele in factor V Leiden G1691A (11.5 vs. 10.5%), mutant T allele in MTHFR C677T (21.5 vs. 21%) and mutant A allele in prothrombin G20210A (3 vs. 2.5%) than controls. Double heterozygosity for two of the three mutations discussed in this study was found in (10 vs. 8%, P = 0.62) in beta-TM patients and controls. The prevalence of factor V Leiden G1691A, prothrombin G20210A and MTHFR C677T mutations was slightly but insignificantly higher in beta-TM patients than controls. beta-TM is a chronic hypercoagulable condition independent of predisposing genetic factors.