Our study was designed to prospectively evaluate the role of the methylenetetrahydrofolate reductase (MTHFR) TT677 genotype, the prothrombin (PT) 620210A mutation, the factor V G1691A mutation in leukemic Turkish children treated according to modified BFM 95 study protocols with respect to the onset at thromboembolic events. Eighty-two consecutive leukemic children investigated had are established inherited prothrombotic risk factor: 29 children showed the MTHFR genotype (heterozygous, n = 22; homozygous, n = 7); 3 showed the heterozygous PT G20210A variant; 16 were carriers of the factor V mutation (heterozygous). In addition, combined prothrombotic defects were found in a further 11 patients the MTHFR mutation was combined with the F V mutation (n = 7), the PT G20210A variant (n = 2). In 7 (8.5%) of these 82 patients, venous thromboembolism occurred. In conclusion, the presence of inherited thrombophilia with Turkish children treated acute lymphoblastic leukemia may be useful for designing targeted primary prevention strategies.