Significance Acute myeloid leukemia (AML) is an aggressive hematologic cancer in which malignant myeloid precursor cells impair hematopoiesis and induce bone marrow failure. Most genes associated with AML are mutated in less than 10% of patients, suggesting that alternative mechanisms of gene disruption contribute to this disease. Here, we demonstrate that alternative splicing provides an additional layer of gene dysregulation and mechanism by which gene function is disrupted in AML. These results demonstrate that classical mutation analysis underestimates the burden of functional gene disruption in AML and highlight the importance of assessing the contribution of alternative splicing to gene dysregulation in human disease.