Histone deacetylases (HDACs) and Histone acetyltransferases (HATs) are two kinds of enzymes, which can, by reversible deacetylation and acetylation, modify the structure and function of chromatin histones that are involved in the regulation of gene expression, as well as many non-histone proteins that regulate cell function in eukaryotes. Compared with HATs, HDACs have attracted more and more attentions for two main reasons over the past few years. First, the relationship of HDACs and cancer, as well as several other diseases has been confirmed. Second, many HDAC inhibitors (HDACi) have entered pre-clinical or clinical research as anti-cancer agents and shown satisfying effects. HDACs, including 18 members at least, are subdivided into 4 classes that generally have high structure similarity and related substrate specificity within classes, but have divergent sequence and different functions even between within classes. This review will introduce the relationship between HDACs and cancer along with the enzymes structure and main function.