Proteinases are enzymes that play important roles in vital cellular and extracellular processes by hydrolytically cleaving peptide bonds in their protein substrates. This cleavage can be non-specific as part of degradation during protein catabolism or highly specific as part of proteolytic cascades and signal transduction events. Several web tools are available for predicting possible cleavage sites in candidate substrates. Here, we compare existing prediction tools with SitePrediction, a novel and user-friendly tool for identifying potential cleavage sites. This prediction is based on known datasets found in the literature, stored in web-accessible repositories or generated by our own experiments. Comparison of the different programs shows that SitePrediction makes it possible to derive more reliable predictions. In addition, this tool allows the use of a wide range of proteinases.