In this chapter, the application of various structure-based modeling techniques and protocols to HDAC enzymes are reviewed. This chapter focuses on structure-based drug discovery approaches on histone deacetylase (HDAC) inhibitors (HDACi) that were applied by the Rome Center for Molecular Design lab. This chapter covers mainly zinc-based HDACi, although some studies on NAD-based HDAC (sirtuin) inhibitors are also included at the end of the chapter. © 2016 Elsevier Inc. All rights reserved.