Mutations in CAPN3/Capn3, which codes for skeletal muscle-specific calpain-3/p94 protease, are responsible for limb-girdle muscular dystrophy type 2A (LGMD2A). Using "knock-in" (referred to as Capn3 CS/CS ) mice, in which the endogenous calpain-3 is replaced with a mutant calpain-3:C129S, that is proteolytically inactive but structurally intact calpain-3, our previous studies demonstrated that loss of calpain-3 protease activity caused muscular dystrophy. However, compared to Capn3 null (Capn3 −/− ) mice, Capn3 CS/CS mice showed less severe dystrophic symptoms. This suggests that calpain-3 also has a non-proteolytic function. This study aimed to elucidate non-protease calpain-3 functions, by comparison of Capn3 CS/CS mice with Capn3 −/− mice. We found that calpain-3 is a component of the sarcoplasmic reticulum (SR), and that calpain-3 interacts with, but does not proteolyze, typical SR components such as ryanodine receptor and calsequestrin. Furthermore, Capn3 CS/CS mice showed that the non-enzymatic role of calpain-3 is required for proper Ca 2+ efflux from the SR to cytosol during contraction of muscles. These results indicate that calpain-3 functions as a non-enzymatic element for the Ca 2+ efflux machinery in the SR rather than as a protease. Thus, defects of the non-enzymatic function of calpain-3 must also be involved in pathogenesis of LGMD2A.