The history of calpain's discovery originates in 1964, when calcium-dependent proteolytic activities caused by a "calcium-activated neutral protease" (CANP) were detected in brain, lens of the eye and other tissues.

The calcium-dependent activity, intracellular localization, and the limited, specific proteolysis on its substrates, highlighted calpain’s role as a regulatory, rather than a digestive, protease.

Shortly thereafter, the activity was found to be attributable to two main isoforms, dubbed μ ("mu")-calpain and m-calpain (or calpain I and II), that differed primarily in their calcium requirements in vitro.

The Human Genome Project has revealed that more than a dozen other calpain isoforms exist, some with multiple splice variants.

[8] Additionally, phosphorylation by protein kinase A and dephosphorylation by alkaline phosphatase have been found to positively regulate the activity of μ-calpains by increasing random coils and decreasing β-sheets in its structure.

[11] Calpain is also involved in skeletal muscle protein breakdown due to exercise and altered nutritional states.

Moreover, the hyperactivation of calpains is implicated in a number of pathologies associated with altered calcium homeostasis such as Alzheimer's disease,[15] and cataract formation, as well as secondary degeneration resulting from acute cellular stress following myocardial ischemia, cerebral (neuronal) ischemia, traumatic brain injury and spinal cord injury.

Increase in concentration of calcium in the cell results in calpain activation, which leads to unregulated proteolysis of both target and non-target proteins and consequent irreversible tissue damage.

Excessively active calpain breaks down molecules in the cytoskeleton such as spectrin, microtubule subunits, microtubule-associated proteins, and neurofilaments.

[19][irrelevant citation] Recently calpain has been implicated in promoting high altitude induced venous thrombosis by mediating platelet hyperactivation.