Fms-like tyrosine kinase 3 (Flt3) is a type III receptor tyrosine kinase. The internal tandem duplication (ITD) of the juxtamembrane region of this receptor is the most prevalent mutation in acute myeloid leukaemia (AML). The silencing mediator of retinoic and thyroid hormone receptors (SMRT) co-repressor recruits histone deacetylases (HDAC) and mediates transcriptional repression by interacting with various transcription factors. We recently reported that Flt3-ITD interferes with the transcriptional and biological action of promyelocytic leukaemia zinc finger transcriptional repressor by dissociating it from SMRT. In this study, we aimed to clarify whether the repressional activity of other well-known oncoproteins, such as AML1/Runx1 (AML1), is also affected by Flt3-ITD. We verified that the repression activity of AML1B, the isoform of AML1, is dependent on HDAC activity by using HDAC inbitor trichostatin A in GAL4 reporter assays. Mammalian two-hybrid assays demonstrated that this protein interacts with SMRT. Furthermore, this AML1B-SMRT interaction was disrupted by the overexpression of Flt3-ITD, leading to the reduction of AML1B repression activity. Additionally, we showed AML1B repression target, p21 (WAF1/CIP1), was aberrantly expressed in Flt3-ITD stably expressed BaF3 cells. Taken together, Flt3-ITD disrupts transcriptional repressor functions resulting in aberrant gene regulation in leukaemic cells.