Introduction: In recent years, Fms-like tyrosin kinase (FLT) 3 has been the subject of several studies as a prognostic marker. Objective: In this study, the presence of FLT3 mutations in childhood acute leukemias patients and their association with prognosis were investigated. Materials and Methods: A total of 120 patients, 80 with acute lymphoblastic leukemia (ALL) and 40 with acute myeloblastic leukemia (AML), were included. Real time polymerase chain reaction methods on a high resolution melting analysis device were used to determine FLT3 mutations. Results: FLT3/ITD (internal tandem duplication) mutations were found in 6 (7.5%) of the patients with ALL and in 9 (22.5%) of those with AML, whereas no FLT3/TKD (trans kinase domain) mutation was evident in any case. There was no difference between the ALL patients positive and negative for FLT3/ITD with regard to overall survival (OS), event free survival (EFS) and disease free survival (DFS) (p=0.37, p=0.23, p=0.023, respectively). However, in FLT3/ITD positive and negative AML patients, there was a statistically significant difference in OS (p=0.0041), but not EFS and DFS (p=0.09, p=0.095, respectively). A significant difference was found between age and FLT3/ITD positivity (p=0.036). Conclusion: We found that FLT3/ITD positivity increased with age and that it was associated with decrease in OS in AML patients, providing further evidence that it is an independent factor negatively influencing prognosis.