The emergence and increasing prevalence of multi-drug resistance bacterial strains represents a clear and present danger to the standard of human healthcare as we know it. The systematic study of modulating biological systems using small molecules (so-called chemical genetics) offers a potentially fruitful means of discovering critically needed new antibacterial agents. Crucial to the success of this approach is the ready availability of functionally diverse small molecule collections. In this feature article we focus upon the use of a diversity-oriented synthesis (DOS) approach for the efficient generation of such compound collections, and discuss the utility of DOS for the discovery of new antibacterial agents.