The same FLT3-internal tandem duplication (ITD) positive clone was detected at diagnosis and relapse, but not at birth, in a child with M1 acute myeloid leukemia. Single nucleotide polymorphism arrays demonstrated that chromosome 13 acquired uniparental disomy, in association with del(9q), represented a progressive event in the course of the disease, and it was responsible for the homozygous FLT3-ITD at relapse.