This chapter proposes a broad review of the methods used for innovative drug design. First, it provides an overview of the objectives for drug development, where the historical growth of drug development cost is compared with the increasing complexity of preclinical candidate pipelines and decreasing new drug proposals and registrations. It discusses the steps involved in the development of a new drug. Then methods for screening drug candidates are reviewed, focusing on three main directions: high-throughput screening, search for new chemical entities, and three-dimensional molecular docking with a known protein-binding pocket. Additionally, this chapter presents search methods for drugs with a new type of action (such as targeted to previously undruggable proteins) and briefly discusses the construction of virtual libraries. Improvement in drug properties is often required, such as lowering toxicity, optimizing distribution in an organism, prolonged action, and drug selectivity. Finally, examples of the ways for drug improvement are discussed.