Free muscle transfers do not generate the same force after transfer as that at the original sites. Light and electron microscopy were used to study serially during 30 weeks the changes at the neuromuscular junction after free muscle transfer of the gracilis muscle in the adult Wistar rat. Under light microscopy, after staining with acetylthiocholine the neuromuscular junction showed changes of degeneration with withdrawal of the innervating axon terminal followed by regeneration and reconstitution of the neuromuscular junction. The newly formed neuromuscular junction still lacked the structural detail seen in the control neuromuscular junction, even after 30 weeks. With the electron microscope, mitochondrial swelling and clumping of the synaptic vesicles were followed by withdrawal of the axon terminal from the muscle membrane on denervation. The infolding of the muscle membrane at the neuromuscular junction became less prominent. With reinnervation the ultrastructure of the junction was only partially reestablished with poorly reconstituted primary and secondary folds of the muscle membrane 30 weeks after the transfer. Failure of complete reformation of the ultrastructure of the neuromuscular junction may provide another explanation for failure of full recovery of skeletal muscle function after free muscle transfer.