Preservation of biochemical processes in muscles is a major challenge in patients with severe peripheral nerve injury. In this chapter, we address the effects of laser irradiation and biochemical transformation in muscle, using in vitro and in vivo experimental models. The authors attempt to explain the possible mechanism of laser phototherapy applied on skeletal muscle on the basis of literature review and new results. A detailed knowledge of the evolution of endplates acetylcholine receptors and creatine kinase activity following laser irradiation can help to understand the therapeutic effect of laser phototherapy on muscle. This study showed that the laser phototherapy increases biochemical activity in intact muscle and thus could have direct therapeutic applications on muscle, especially during progressive atrophy resulting from peripheral nerve injury.