The MEROPS database includes over 39 000 cleavages in substrates (synthetic and naturally occurring) which have been collected from the literature. These are classified as physiological or non-physiological, depending on whether the substrate is naturally occurring and if it is in native conformation. At least one substrate is known for 45% of the different peptidases identified in the MEROPS database. Displays in the database give insights into peptidase specificity and to the conservation of cleavage sites amongst orthologous proteins. The data provide a substantial training set for algorithms to predict peptidase substrates and cleavage positions in those substrates. The data may also be useful for the design of inhibitors and engineering novel specificities into peptidases. By examining the conservation of cleavage sites in protein substrates in terms of peptidase substrate binding sites, it is clear that there are a number of cleavages where atypical replacements occur. Many of these can be explained by gene build or sequencing errors, inserts or deletions in the region around the cleavage site, or the alignments contain one or more paralogues in which cleavage may be absent or different. In a few cases it is possible that more than one peptidase is involved in processing, or there may not be enough known substrates for some peptidases to be sure that an atypical replacement is really unacceptable. A number of substrate cleavages that may be fortuitous and not of any physiological relevance have been identified.