Introduction. Acute myeloid leukemia (AML) is a heterogeneous disease and about one third do not have evident genetic abnormalities. The mutation of specific molecular markers such as fms-like tyrosine kinase 3 (FTL3) internal tandem duplication (ITD) and nucleophosmin (NPM1) are associated with an adverse and favorable prognosis, respectively. Objective. To determine the prevalence of FLT3/ITD and NPM1 in Chilean children under 18 years and its association with clinical data and prognosis. Results. Two hundred and thirty-two children with AML were studied between 2011-2017, median 8.6 years (range 1 month-18). Acute promyelocytic leukemia (APL) was diagnosed in 29%. FLT3/ITD mutated in non-promyelocytic AML was 10% (14/133), and FLT3/TKD 3.7% (2/54). In APL was 25.4% (16/63). In non-promyelocytic AML, FLT3/ITD mutated was associated with high leucocyte count, median 28.5 xmm3 (n=14) versus 19.4 xmm3 (n=119), (p=0.25) in unmutated cases. In APL was, median 33.6 xmm3 (n=15) versus 2.8 xmm3 (n=47), (p<0.001). Five-year overall survival (OS) in non-promyelocytic AML with unmutated and mutated FLT3/ITD, 62.7% and 21.4%, (p<0.001); 5-year event free survival (EFS) 79.5% and 50%, (p <0.01). Five-year OS in APL with unmutated and mutated FLT3/ITD was 84.7% and 62.5%, (p =0.05); while 5-year EFS was 84.7% and 68.8% (p =0.122). NPM1 mutation was observed in 3.2% (5/155), all non-promyelocytic AML with normal karyotype. Conclusion. FLT3/ITD mutation was observed more frequently in APL and associated with higher white cell count at diagnosis. However, the most important finding was that FLT3/ITD mutation was associated with lower survival in non-promyelocytic AML.