Histone deacetylase inhibitors (HDACi) are an emerging class of novel anti-cancer drugs that cause growth arrest, differentiation and apoptosis of tumor cells. In addition, many advances have been made in understanding the immunoregulation of Toll-like receptors, NOD-like receptors and interferons that have recently generated new momentum for the study of HDACi in immunity as a whole, and in the regulation of these innate signaling pathways specifically. HDACi have shown promise as new anti-inflammatory and immunosuppressant agents. They have also demonstrated great potency and relative selectivity in various human/animal models of inflammatory diseases. This review focuses on recent progress and the current state of HDACi knowledge, as well as the molecular mechanisms and therapeutic potential of HDACi for the treatment of inflammatory diseases and cancers.Immunology and Cell Biology advance online publication, 15 November 2011; doi:10.1038/icb.2011.92.