The present review compiles the current combinatorial methodologies for the study of enzyme activity and inhibition. Modern combinatorial technology realises that the most important criterion for successful generation of valuable drug candidates is the integration of all aspects of the processes involved. Therefore many screening formats, analytical methods and synthetic technologies are required for different purposes in the discovery process. Methods involving the screening of discrete sets of compounds in well plates perfectly complements solid-phase screening of millions of compounds or large compound arrays and each technique has inherent virtues and difficulties. This review attempts to emphasise the features of each of the available methods and provides recommendations for the selection of a particular technology. The combinatorial methods for the investigation of protease activity and inhibition provide a powerful set of tools to exploit proteolytic enzymes as drug targets. The use of combinatorial techniques for the differentiation of related enzymes with similar specificity, thus facilitating the development of selective drugs with little or no unwanted interaction with non-target enzymes, is also described. The review concludes that the methods complement each other well and that selection of the optimal technology may well depend on the nature of the problem investigated. The potency of combinatorial enzyme screening is rapidly increasing with the development of versatile solid-phase chemistries, enzyme compatible polymers and surfaces, analytical nano- and encoding techniques and, not the least, extremely sensitive and robust assays based mainly on fluorescence and FRET techniques.