Biology oriented synthesis (BIOS), is an approach to efficiently identify compound classes to be used as probes or tools for chemical biology research as well as starting points for medicinal chemistry programs. As chemical space is enormously large and cannot be not be exhaustively covered using solely synthetic chemistry, methods which direct and pin-point biologically relevant areas are highly sought. Such methods would also serve as hypothesis-generating tools, inspiring the syntheses of novel, bioactive molecular scaffolds. Building on the notion of structural conservatism in the evolution of proteins and natural products, BIOS utilizes a hierarchical classification of bioactive compound classes depending on the structural and categorical classification of bioactivity, for instance using the Scaffold Hunter software as a navigational tool in chemical space. Biologically-relevant scaffolds inspire and direct the synthesis of BIOS libraries which have enriched bioactivities, facilitating the discovery of the highly sought after small molecules which allow the perturbation of complex biological phenomena and may serve as starting points for drug discovery programs. This chapter will elaborate on the underlying reasoning for the development of BIOS, as well as its current and possible future applications.