The family of calpains (CANP or calcium activated neutral proteases) and their endogenous inhibitor calpastatin have been implicated in many neural functions; however, functional distinctions between the major calpain isoforms, calpain I and II, have not been clearly established. In the present study we analyzed the gene expression patterns for calpain I and II and calpastatin in mouse brain and spinal cord by measuring both their mRNA and protein levels. Our results show that the overall mRNA level measured by competitive reverse transcription polymerase chain reaction for calpain II is 15-fold higher and for calpastatin is three-fold higher than that for calpain I. Overall, both mRNA and protein expression levels for the calpains and calpastatin showed no significant difference between the spinal cord and the brain. The cellular distributions of mRNA for calpain I or calpastatin, measured by in situ hybridization, are relatively uniform throughout the brain. In contrast, calpain II gene expression is selectively higher in certain neuron populations including pyramidal neurons of the hippocampus and the deep neocortical layers, Purkinje cells of cerebellum, and motor neurons of the spinal cord. The motor neurons were the most enriched in calpain message. Motor neurons possessed 10-fold more calpain II mRNA than any other spinal cord cell type. The differential distribution of the two proteases in the brain and the spinal cord at the mRNA level indicates that the two calpain genes are differentially regulated, suggesting that they play different physiological roles in neuronal activities and that they may participate in the pathogenesis of certain regional neurological degenerative diseases.