Peripheral vascular occlusive diseases are frequently observed in humans, and studies with animal models have been largely used. However the effects of sustained lower limb ischemia on normal and regenerating hindlimb skeletal muscles are not well known in the mouse model. Therefore prolonged unilateral hindlimb ligation was generated by femoral artery ligation. Normal (myotoxic-untreated) and regenerating (myotoxicreated) ischemic muscles were studied by analyses of the in situ contractile properties and histological parameters. Concerning normal mouse muscles, we found that femoral artery ligation reduced hindlimb perfusion and altered muscle structure and function. Thus 7 days after ligation, maximal tetanic force was reduced by about 70%, (p < 0.05). By 56 days after ligation, muscle weights and cross-section areas of muscle fibers were still reduced (p < 0.05). Concerning myotoxic treated muscles, we report that ligation reduced the recovery of muscle weight and maximal tetanic force and increased fatigue resistance at 56 days (p < 0.05). In conclusion, our results demonstrate that sustained peripheral arterial insufficiency in mice induces long-term as well as acute detrimental effects in both normal and regenerating muscles.