运用一小组化学构建基因，以多种方式结合，用标准化学方法建立大的与医药相关的化合物的文库，以用于新药的筛选。组合化学与大规模筛选相结合用于识别与治疗用靶蛋白结合的化合物即潜在新药。最初的新的结合物称为"标的"，标的然后被优化为"先导物"并最终发展成为真正的药物。组合化学策略依赖于欲构建文库的大小、和多样性，试剂的有效性和成本和化学合成的类型。总体而言，有两种形式的组合文库合成，"液相"合成和"固相"合成，对后者来说，化学反应是与附在支持物（如：玻珠和柱子）上的一种或多种试剂发生的。这两种文库合成方法都有各自的优、缺点；液相合成允许很多化学反应进行；然而所形成的文库必然是液相混合物，必须能够从组合混合物中区别单个化合物。固相合成的优点是单个化合物在合成中是在空间上分开的；然而必须发展新的化学反应应用于固相合成。

The use of a small set of chemical building blocks, combined together in multiple ways, using standard chemistries, to create large libraries of medicinally relevant compounds that may be screened for potential new drugs. Combinatorial chemistry is used in tandem with high-throughput screening to identify compounds that bind to a therapeutic target protein and are thus potential new drugs. Initial new binders are called“hits”; hits can then be optimized into“leads”for further development into bona fide drugs. Combinatorial chemistry strategies depend on the size and diversity of the library to be designed, the availability and cost of the reagents (building blocks), and the type of chemical syntheses being attempted. In general, two forms of combinatorial library synthesis exist,“liquid-phase”synthesis and“solid-phase”synthesis; in the latter the chemistries are performed with one or more of the reagents attached to an inert solid support such as a bead or column. Each of the two methods of library synthesis has its own advantages and disadvantages; Liquid-phase synthesis allows many more standard chemistries to be performed (most chemical synthesis steps have been developed for individual compound synthesis in the liquid phase); however, the resultant library is necessarily a mixture of compounds within the liquid, and deconvolution strategies must be applied to identify individual compounds from the combinatorial mixture. Solid-phase synthesis has the advantage that individual compounds are spatially separated during synthesis; however, novel chemistries must be developed in order to be useable in the solid phase.