BACKGROUND: Fms-like tyrosine kinase 3 internal tandem duplication (FLT3 ITD) mutation is related to poor prognosis in normal-karyotype acute myeloid leukemia (AML). However, the prognostic significance of the mutation at relapse has not been adequately investigated. We investigated the prognostic significance of the FLT3 ITD mutation at relapse in normal-karyotype AML patients. METHODS: We analyzed 69 normal-karyotype AML patients, in whom paired bone marrow samples taken at initial diagnosis and subsequent relapse were analyzed for the FLT3 ITD mutation at the Asan Medical Center between 1995 and 2009. RESULTS: Forty patients showed a persistent wild-type genotype, 11 showed the FLT3 ITD mutation at diagnosis and relapse, and 9 lost and another 9 acquired the mutation at relapse. The mutation status at relapse affected the overall survival (OS), with the mutation group showing shorter OS and survival after relapse than the wild-type group did (P<0.001 and P<0.001, respectively), despite having received more frequent stem cell transplantation after relapse than the wild-type group did. However, no difference was detected in the OS and survival after relapse with regard to the mutation status at diagnosis. CONCLUSION: The patients with FLT3 ITD mutation at relapse showed poorer prognoses than those without the mutation. However, mutation status at diagnosis did not affect the outcome. These results suggest that, in normal-karyotype AML patients with relapse, the prognostic significance of FLT3 ITD mutation at relapse is greater than that of the mutation status at diagnosis.