Proteomic and genomic discoveries have identified vast numbers of new drug targets for investigation. In the quest to discover drugs that modulate the function of these targets, identification of small-molecule drug leads is one of the earliest steps. Structure-based drug design has emerged as a valuable, inexpensive, and rapid computational resource that identifies lead compounds that are complementary to the structure of the target. Leads identified through this process are biologically evaluated and "hit compounds" with affinity and activity are further optimized. This chapter introduces the process of structure-based drug design, including preparation of the ligand database, preparation of the target structure, docking and scoring, and evaluation.