The gene expression profiles of 146 novel ESTs were characterized in newborn and adult rat brains via radioactive in situ hybridization. Using Euclidean metrics and hierarchical clustering tools the brain expression profiles obtained clustered into seven synexpression groups. The groups were: I, non-detectable expression (68 ESTs); II, low expression in hippocampus (40 ESTs); III, low expression in adult, high expression in newborn (two ESTs); IV, medium expression throughout brain (31 ESTs); V, high expression throughout brain (three ESTs); VI, selective high expression in hippocampus, caudate and putamen (one EST); VII, selective high expression in hippocampus (one EST). Five ESTs were expressed in the striatum and three responded transcriptionally to neuroleptic and neuroprotective drug treatments, suggesting that this approach could be used to detect novel drug targets. These results provide a useful starting point to explore the functional genomics of genes without known functions forthcoming from various genome projects. © 2002 Elsevier Science Ltd.