The genomic characteristics of such deletions remain largely undefined, hindering further understanding of the clinical significance of the deletions.<h4>Case presentation</h4>We report here two AML cases with inv(16) and deletion of the 5'<i>MYH11</i>/3'<i>CBFB</i> gene fusion, which were characterized by chromosome, FISH, and single nucleotide polymorphism (SNP) microarray analyses. The gene discussed is CBFB; the disease is acute myeloid leukemia.