5-HT4 receptors are implied in various peripheral and central functions, such as gastro-intestinal tonicity and secretions, as well as the modulation of emotional behaviour and cognitive mechanisms. Several years ago, our research center (CERMN) has launched a program for the discovery of new 5-HT ligands based on biological tests done in a screening center. This program led to new families of 5-HT4 ligands in the past years.1,2 The CERMN currently owns a chemolibrary of more than 10000 compounds including one thousand 5-HT4 binding data. In this study we analyse the performance of some fingerprint descriptors, metrics and hierarchical methods to classify compounds according to their activity.