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Skeletal muscles have a tremendous capacity for repair and regeneration in response to injury. This capacity for regeneration is largely due to a myogenic stem cell population, termed satellite cells, which are resident in adult skeletal muscles. In order to decipher the mechanisms that govern myogenic stem cell quiescence, activation, differentiation, and self-renewal, a reproducible injury model is required. Therefore, we have utilized the delivery of the myonecrotic agent, cardiotoxin, to examine the molecular mechanisms of myogenic stem cells in response to injury. Here, we describe our experience using cardiotoxin as a potent myonecrotic agent to study skeletal muscle regeneration. We provide a detailed protocol to examine skeletal muscle injury and regeneration using morphological analyses.