Ninety-eight newly diagnosed cases of PML-RARalpha positive APL were treated with a regimen of single agent ATO. FLT3 activating mutations were seen in 33% and an additional cytogenetic finding was noted in 23.2%. FLT3 activating mutations were significantly associated with a bcr3 PML-RARalpha isoform (p=0.012) and a delay in achieving a molecular remission (p=0.022). Neither FLT3 activating mutations nor secondary cytogenetic changes had an impact on clinical outcome.