運用一小組化學構建基因，以多種方式結合，用標準化學方法建立大的與醫藥相關的化合物的文庫，以用于新藥的篩選。組合化學與大規模篩選相結合用于識別與治療用靶蛋白結合的化合物即潛在新藥。最初的新的結合物稱為"標的"，標的然后被優化為"先導物"并最終發展成為真正的藥物。組合化學策略依賴于欲構建文庫的大小、和多樣性，試劑的有效性和成本和化學合成的類型。總體而言，有兩種形式的組合文庫合成，"液相"合成和"固相"合成，對后者來說，化學反應是與附在支持物（如：玻珠和柱子）上的一種或多種試劑發生的。這兩種文庫合成方法都有各自的優、缺點；液相合成允許很多化學反應進行；然而所形成的文庫必然是液相混合物，必須能夠從組合混合物中區別單個化合物。固相合成的優點是單個化合物在合成中是在空間上分開的；然而必須發展新的化學反應應用于固相合成。

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.