In high-risk myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), blasts constitutively activate the antiapoptotic transcription factor nuclear factor-κB (NF-κB). Here, we show that this NF-κB activation relies on the constitutive activation of the IκB kinase (IKK) complex, which is formed by the IKKα, IKKβ and IKKγ/NF-κB essential modulator (NEMO) subunits. A cell-permeable peptide that mimics the leucine zipper subdomain of IKKγ, thus preventing its oligomerization, inhibited the constitutive NF-κB activation and induced apoptotic cell death in a panel of human MDS and AML cell lines (P39, MOLM13, THP1 and MV4–11). Small interfering RNA-mediated knockdown of the p65 NF-κB subunit or the three IKK subunits including IKKγ/NEMO also induced apoptotic cell death in P39 cells. Cell death induced by the IKKγ/NEMO-antagonistic peptide involved the caspase-independent loss of the mitochondrial transmembrane potential as well as signs of outer mitochondrial membrane permeabilization with the consequent release of cytochrome c, apoptosis-inducing factor and endonuclease G. Primary bone marrow CD34+ cells from high-risk MDS and AML patients also succumbed to the IKKγ/NEMO-antagonistic peptide, but not to a mutated control peptide. Altogether, these data indicate that malignant cells in high-risk MDS and AML cells critically depend on IKKγ/NEMO to survive. Moreover, our data delineate a novel procedure for their therapeutic removal, through inhibition of IKKγ/NEMO oligomerization.