Background and Objective: Evaluation of degenerative changes of motoneurons and their related synapses can be useful in understanding the mechanisms of neurodegenerative diseases and their potential treatment. The present electron microscopic and immunohistochemical study investigates the axotomy-induced changes of adult spinal motoneurons up to 3 months following sciatic nerve transection. Materials and Methods: Following unilateral mid-thigh sciatic transection in adult rats, the synaptophysin expression and ultrastructure of synapses in ventral horn of related spinal cord segments were studied 1 day, 1 week, 1 month, and 3 months postoperatively. In all groups the unaxotomized side of spinal cord was considered as control. The pattern of synaptophysin immunolabeling was classified into intact, partial, diffused, and negative types. Results: In 1 week and 1 month groups, the intact pattern decreased and the other 3 patterns increased, whereas 3 months postoperatively the patterns changed vice versa, i.e. intact pattern increased and the other 3 decreased. Electron microscopic studies indicated consistent ultrastructural changes such as synaptic vesicle displacement, synaptic membrane irregularity and synaptic stripping, which were most prominent after 1 month and declined in 3 month group. Conclusion: The present data indicate that following axon injury in adult motoneurons, synapses undergo obvious changes in ultrastructure and synaptophysin distribution, which increase up to 1 month postoperatively, and if the cell survives the insult the changes will attenuate and return to normal conditions thereafter.