Fms-like tyrosine kinase 3 (FLT3) performs a vital role in the pathogenesis of hematopoietic malignancies.Therefore in recent times, the focus of several studies was on use of FLT3 as a prognostic marker. The presentstudy investigated the molecular characterization and incidence of FLT3 mutations in acute leukemia patients inPakistan. A total of 55 patients were studied, of which 25 were suffering from acute lymphoblastic leukemia (ALL)and 30 were suffering from acute myeloid leukemia (AML). The polymerase chain reaction demonstrated FLT3/ITD mutations in 1 (4%) of 25 ALL patients, a male with the L2 subtype. In AML cases the rate was 4 (13.3%) of30, three males and one female. The AML-M4 subtype was found in three and the AML M2 subtype in the other.In the AML cases, a statistically significant (p=0.009) relationship was found between WBC (109/L) and FLT3/ITD positivity. However, no significant relationship was found with other clinical parameters (p>0.05). In acutemyeloid leukemia (AML) FLT3/ITD+ mutation was more prevalent in elderly patients 31-40 age groups, 21-30and 51-60 age groups respectively. In acute lymphoblastic leukemia (ALL) statistically no significant relationshipwas found between clinical features and FLT3/ITD positivity (p>0.05). However, in acute lymphoblastic leukemia(ALL) FLT3/ITD+ mutation was more commonly found in age groups of 21-30.