Spinal cord injury (SCI) is a serious neurological disorder that debilitates mostly young people. Unfortunately, we still do not have suitable therapeutic agents for treatment of SCI and prevention of its devastating consequences. However, we have gained a good understanding of pathological mechanisms that cause neurodegeneration leading to paralysis or even death following SCI. Primary injury to the spinal cord initiates the secondary injury process that includes various deleterious factors for ultimate activation of different cysteine proteases for degradation of cellular key cytoskeleton and other crucial proteins for delayed death of neurons and glial cells at the site of SCI and its penumbra in different animal models. An important aspect of SCI is the increase in intracellular free Ca(2+) concentration within a short time of primary injury. Various studies in different laboratories demonstrate that the most important cysteine protease for neurodegeneration in SCI is calpain, which absolutely requires intracellular free Ca(2+) for its activation. Furthermore, other cysteine proteases, such as caspases and cathepsin B also make a contribution to neurodegeneration in SCI. Therefore, inhibition of cysteine proteases is an important goal in prevention of neurodegeneration in SCI. Studies showed that individual inhibitors of cysteine proteases provided significant neuroprotection in animal models of SCI. Recent studies suggest that physiological hormones, such as estrogen and melatonin, can be successfully used for prevention of neurodegeneration and preservation of motor function in acute SCI as well as in chronic SCI in rats.