The modern drug discovery process involves a hypothesis-oriented approach to target selection and medicinal chemistry design. Recent advances in human genetics, systems biology and chemical proteomics enable medicinal chemists to play a significant role in generating and supporting the initial hypothesis underpinning a drug discovery project. Diverse lead seeking strategies from high throughput screening to targeted subset assessment, ligand-based pharmacophore searches, target-based virtual screens and fragment based approaches provide medicinal chemists more control over the source of initial chemical equity. Powerful in silico predictive tools enabling ADME and safety property prediction, coupled with multiparameter optimization techniques, enable a more rational approach to lead optimization using a holistic view of drug properties. Upon selecting a clinical candidate, medicinal chemists become knowledgeable partners in understanding and solving physical form issues, applying new formulation technologies and addressing synthetic scalability. As the drug candidate progresses through preclinical and clinical studies, knowledge gained around safety, pharmacokinetics and efficacy is incorporated into future drug discovery efforts for backup compounds and other related programs. The medicinal chemist's role in conceiving the initial compound design and providing matter that drives drug discovery within a project gives them a prominent role from idea inception to clinical studies.