•RUNX1 isoform disequilibrium toward RUNX1A and its interaction with MYC:MAX are key in the pathogenesis of trisomy 21–associated ML.•Restoration of RUNX1A:RUNX1C equilibrium and pharmacological interference with MYC:MAX dimerization reverses the oncogenic phenotype. Display omitted Gain of chromosome 21 (Hsa21) is among the most frequent aneuploidies in leukemia. However, it remains unclear how partial or complete amplifications of Hsa21 promote leukemogenesis and why children with Down syndrome (DS) (ie, trisomy 21) are particularly at risk of leukemia development. Here, we propose that RUNX1 isoform disequilibrium with RUNX1A bias is key to DS-associated myeloid leukemia (ML-DS). Starting with Hsa21-focused CRISPR–CRISPR-associated protein 9 screens, we uncovered a strong and specific RUNX1 dependency in ML-DS cells. Expression of the RUNX1A isoform is elevated in patients with ML-DS, and mechanistic studies using murine ML-DS models and patient-derived xenografts revealed that excess RUNX1A synergizes with the pathognomonic Gata1s mutation during leukemogenesis by displacing RUNX1C from its endogenous binding sites and inducing oncogenic programs in complex with the MYC cofactor MAX. These effects were reversed by restoring the RUNX1A:RUNX1C equilibrium in patient-derived xenografts in vitro and in vivo. Moreover, pharmacological interference with MYC:MAX dimerization using MYCi361 exerted strong antileukemic effects. Thus, our study highlights the importance of alternative splicing in leukemogenesis, even on a background of aneuploidy, and paves the way for the development of specific and targeted therapies for ML-DS, as well as for other leukemias with Hsa21 aneuploidy or RUNX1 isoform disequilibrium. Trisomy 21 (+21) is a frequent alteration in acute myeloid leukemias (AML) and constitutive in Down syndrome myeloid leukemia (ML-DS). In this Plenary Paper, Gialesaki et al show that ML-DS blasts are dependent on RUNX1 and reveal that disequilibrium among RUNX1 transcripts with disproportionately increased level of RUNX1A is pivotal for DS leukemogenesis and prominent in sporadic AML. This validates a new model for the early stages of ML-DS development and suggests new therapeutic targets for +21 AMLs in general.