Neural circuits within the vertebrate brain are composed of highly diverse cell types. The exact extent of this diversity is a matter of continuing debate. For example, do cortical interneurons comprise a few, dozens or >100 distinct cell types? Recently, several groups have used microarrays to measure genome-wide gene expression profiles for specific neuronal cell types. These methods can offer an objective basis for neuronal classification. In this review, we argue that this approach should now be carried out more broadly and that it should be coupled to large-scale efforts to generate mouse driver lines in which tools for genetic manipulation, such as the Cre recombinase, are expressed in identified cell types within the brain. This would enable neuroscientists to begin to investigate more systematically the roles of specific genes in establishing particular cellular phenotypes, and also the roles of particular cell types within brain circuits. This review is part of the TINS special issue on The Neural Substrates of Cognition.