Histone Deacetylases (HDACs) are a group of enzymes closely related to sirtuins. They catalyze the removal of acetyl groups from lysine residues in histones and non-histone proteins, resulting in transcriptional repression. There are three classes of HDACs; classes 1, 2 and 4, which are closely related Zn2+-dependent enzymes. HDACs are ubiquitously expressed and they can exist in the nucleus or cytosol. Class 1 HDACs are predominantly nuclear while class 2 HDACs shuttle between the nucleus and cytosol. HDAC6 is a class 2 histone deacetylase enzyme localized to the cytoplasm and associated with the microtubule network. It is involved in the regulation of many cellular processes, including cell migration, immune synapse formation, viral infection, and degradation of misfolded proteins. HDAC6 contains two tandem catalytic domains that facilitate the deacetylation of multiple protein substrates, including histones and non-histone proteins such as tubulin, cortactin, and HSP90. In addition to its role as a protein deacetylase, HDAC6 functions as a component of the aggresome, a inclusion body that forms in response to an accumulation of misfolded or partially denatured proteins. Formation of the aggresome is a protective response that sequesters cytotoxic protein aggregates for eventual autophagic clearance from the cell. HDAC6 contains a zinc finger ubiquitin-binding domain that binds both mono- and poly-ubiquitinated proteins. It facilitates the transport of misfolded proteins to the aggresome. HDAC6 is also required for subsequent recruitment of the autophagic machinery and clearance of aggresomes from the cell. Thus, HDAC6 plays a key role in the protection against the deleterious effects of pathological protein aggregation that occurs in various diseases, such as neurodegenerative Huntington’s disease.