Problem A useful technique for characterizing connectivity between nerve and muscle involves prolonged electrical stimulation of nerve fibers to deplete glycogen in their target muscle fibers. Depleted muscle fibers appear blank when stained by the PAS technique. Unfortunately, results are inconsistent over a wide range of stimulus paradigms. The aim of this study was to identify other factors that may impact glycogen depletion. Methods Glycogen depletion was examined in the rat medial gastrocnemius muscle because of the presence of aerobic fiber types I and IIA, which are resistant to depletion. Tension and EMG were monitored during maximal stimulation of transected sciatic nerve with a 333 msec pulse train delivered at 40 Hz every second over a period of 1 hour. Once an effective paradigm was identified, depletion of an entirely aerobic muscle (i.e., soleus) was evaluated. Results Animals maintained in a light plane of anesthesia with a steady rate of pentobarbital IP infusion showed an average depletion of only 72%. Animals administered a progressively increasing level of anesthesia with continued stimulation until complete loss of muscular response showed a significantly greater depletion of 96%. However, when this paradigm was applied to the soleus, only 37% of the muscle depleted. Further investigation determined that co-contraction of gastrocnemius with soleus resulted in unloading of the slower soleus. Disruption of the gastrocnemius insertion on the Achilles tendon shifted the load to the soleus and increased soleus depletion to 93%. Conclusion Muscle fibers of any motor unit type can be identified with 93–96% accuracy when nerve stimulation is applied to an isometrically loaded muscle that is in a state of progressive barbiturate anesthesia. Significance Glycogen depletion provides a method for identifying the number, types, and distribution of muscle fibers in a muscle that have reinnervated, important in the assessment of nerve regeneration. Support NIH grants R01 DC001149 and R01 DC008429.