New developments in cheminformatics are reviewed in the perspective of combinatorial chemistry and drug discovery. One of the most important trends is the realization that the ability to generate compounds in large numbers may not, in isolation, be helpful. It is more important to enrich combinatorial libraries with compounds which, if found to be active, can be quickly developed into viable drug candidates. Library design tools are being created that incorporate an accumulated medicinal chemistry experience necessary to produce compounds with desirable pharmacological properties. The development of methods to ensure chemical accessibility of designed libraries has also become important because of the need to integrate all steps of library generation, from design to synthesis, into one automated high-throughput process.