Background and Objective: Sciatic nerve transection is characterized by a rapid wave of motoneuron death associated with progressive synaptic lesions. The purpose of this study was to evaluate the long term synaptic changes. Materials and Methods: This basic study was carried out on paraffin- or resin-embedded tissue blocks for evaluation of synaptophysin and choline acetyl transaferase (CHAT) immunoreactivities and the ultrastructural changes in the synapses of spinal motoneurons following sciatic nerve axotomy in the newborn rats. Results: The results showed that there was a progressive decrease in the percentage of survived motoneurons and high percentage of chromatolytic motoneurons. There was also a high percentage of degenerated motoneurons with dotted pattern synaptophysin immunoreactivity, low percentage of intact motoneurons with complete synaptophysin labeling, and high percentage of motoneurons with low CHAT labeling. The ultrastructural study showed that there were many motoneurons with synaptic pathological changes including irregularity of the synaptic membrane and displacement of synaptic vesicles. Conclusion: The findings of this study indicate that there is a delayed synaptic lesion in axotomized motoneurons of newborn rats.