Objective To reveal the important role of aberrant splicing in cancer and to identify differential expressing isoforms and differential alternative splicing events between acute myeloid leukemia ( AML) and chronic myeloid leukemia (CML).Methods Based on whole transcriptome sequencing of CML (K562) and AML(THP1 and HL-60) cells,TopHat, MATS and Cufflinks were used to identify alternative splicing events and alternative splicing isoforms and analyze differenti -al expression of isoforms and genes .Results A total of 130 genes were identified to be highly expressed in CML and 80 genes in AML cells .Also, 337 differential expressed isoforms and 35 specific alternative splicing events between AML and CML cells were identified.Conclusion There are significant differences in alternative splicing isoforms and events between AML and CML cells.Leukemia-associated alternative splicing events can be used as potential tumor markers or drug targets.