Since the modest beginnings of its discovery in the late 1970’s, ubiquitination has emerged as a central and critical process involved in the regulation of virtually all cellular activities. Ubiquitin (Ub) is a small (76 kDa) highly conserved protein ubiquitously expressed in eukaryotic organisms. The conjugation of ubiquitin to proteins is an important means to regulate protein function by targeting tagged proteins for proteasomal degradation or by modifying their activity. The modification of target proteins by ubiquitination is reversible, and the removal of Ub can rescue proteins from degradation or re-modulate their activity. The deconjugation of ubiquitin is accomplished by the deubiquitinating enzymes (DUBs). The majority of DUBs in the human genome belong to the ubiquitin specific protease (USP) subclass of DUBs. Structurally, USPs contain a common catalytic domain that consists of two short well-conserved motifs, called Cys and His boxes. Deubiquitination by USPs has been established as an important aspect of many cellular processes and is viewed as a critical regulatory mechanism in the cell. Research on the regulation of these enzymes is only in its beginning phase, and more information on this aspect of USP biology will help to further delineate the cycle of ubiquitination.