Calcineurin belongs to the family of Ca2+/calmodulin-dependent protein phosphatase, protein phosphatase 2B. Calcineurin is the only protein phosphatase which is regulated by a second messenger, Ca2+. Furthermore, calcineurin is highly localized in the central nervous system, especially in those neurons vulnerable to ischemic and traumatic insults. For these reasons, calcineurin is considered to play important roles in neuron-specific functions. Recently, on the basis of the finding that FK506 and cyclosporin A serve as calcineurin-specific inhibitors, this enzyme has become the subject of much study. It is clear that calcineurin is involved in many neuronal (or non-neuronal) functions such as neurotransmitter release, regulation of receptor functions, signal transduction systems, neurite outgrowth, gene expression and neuronal cell death. In this review, we describe the calcineurin functions, functions of the substrates, and the pathogenesis of traumatic and ischemic insults, and we discuss the potential role of calcineurin. There are many similarities in traumatic and ischemic pathogenesis of the brain in which the release of excessive glutamate is followed by an intracellular Ca2+ increase. However, the intracellular cascade which leads to neuronal cell death after the release of excess Ca2+ is unclear. Although calcineurin is thought to be a key toxic enzyme on the basis of studies using immunosuppressants (FK506 or cyclosporin A), many of the functions of the substrates for calcineurin protect against neuronal cell death. We concluded that calcineurin is a bi-directional enzyme for neuronal cell death, having protective and toxic actions, and the balance of the bi-directional effects may be important in ischemic and traumatic pathogenesis.