Proteomic tools offer a new platform for studies of complex biological functions involving large numbers and networks of proteins. Intracellular networks of proteins perform key functions in neurons and glia. The unicellular eukaryote Saccharomyces cerevisiae has been the prototype for eukaryotic proteomic studies, and when combined with genomics, microarrays, genetics, and pharmacology, new insights into the integrated function of the cell emerge. The anatomical complexity of the nervous system both in cell types and in the vast number of synapses introduces novel technical and biological issues regarding the subcellular organization of protein networks. Here we will discuss the technology of proteomics and its applications to the nervous system.