Protein kinases play a crucial role in the pathogenesis of inflammatory bowel disease (IBD), the two main forms of which are ulcerative colitis and Crohn's disease. In this article, we will review the mechanisms of involvement of protein kinases in the pathogenesis of and intervention against IBD, in terms of their effects on genetics, microbiota, mucous layer and tight junction, and the potential of protein kinases as therapeutic targets against IBD.© 2014 Baishideng Publishing Group Inc. All rights reserved.Key words: Inflammatory bowel disease; Protein kinase; Barrier function; Microbiota; Genetics Core tip: The roles of protein kinases in the pathogenesis and intervention of inflammatory bowel diseases (IBD) are emerging. In this article, we will review the specific roles of different protein kinases in the pathogenesis of IBD, classify these protein kinases into different categories based on their fundamental functions in IBD, and describe substantial new mechanistic insights into the pathogenesis of IBD, highlighting protein kinases as potential intervention targets against IBD.