A single muscle of Wistar female rats, either soleus or peroneus longus, was immobilized by fixing its cut distal tendon to the bone during 8 weeks. We observed a transitory weight loss in both muscles; the mean fiber cross-sectional area (CSA) showed a reduction at day 30, followed by an increase at day 60. The time course of the activation of the immobilized muscle was evaluated by recording the chronic electromyographic (EMG) activity during short periods (1 min every other day) of treadmill locomotion. During immobilization, the integrated EMG amplitude of the soleus increased, reaching a maximum at 4 weeks, but remained close to control values during 8 weeks for the peroneus. The median frequency (MF) of the power density spectrum of the soleus EMG was not statistically different between immobilized and control muscles, while MF of the immobilized peroneus EMG was permanently higher than that of control muscles. This suggests two different modes of adaptation in motor unit command, depending on the muscle profile, which could be concomitant with the restoration of muscle fibers CSA after 8 weeks.