Among those enzymes that regulate gene expression, histone deacetylases (HDACs) play important roles in cell cycles.  Extensive studies were carried out in the field of HDACs and the applications of HDAC  inhibitors (HDACIs) as chemotherapeutic interventions for diverse diseases.  HDACIs have moved from   laboratories to clinic uses.  Huge bodies of related research results were well documented and dispersed in   literature.  According to our understanding, HDACIs can be broadly classified as hydroxamic acids, cyclic tetrapeptides, short chain fatty acids, benzamides and electrophilic ketones.  Herein, we are going to review the design and their structure-activity relationships of HDACIs and according to their structural catalogs.