The aim of this study was to compare the ultrastructural alterations of the muscle and nerve that appear following injection of freshly reconstituted and stored botulinum toxin A. Fifteen New Zealand white rabbits were assigned to 6 groups, and anterior auricular muscle was used for injections. Group I did not receive any injection and group 2 received saline injection. Groups 3 and 5 received fresh botulinum; muscles and motor nerves were harvested at 5 days and 12 weeks, respectively. Groups 4 and 6 received stored botulinum; muscles and motor nerves were harvested at 5 days and 12 weeks, respectively. Alterations in muscle and nerve ultrastructure were evaluated with electron microscopy. Degeneration findings in muscle after botulinum toxin injection revealed no significant difference between freshly reconstituted and stored toxin in the early period. When stored toxin was used, atrophic changes in the muscle were less severe than the fresh toxin at 3 months. On nerve evaluation, fresh toxin displays signiticant acute changes on nerve ultrastructure; however, fresh and stored toxin shows similar degeneration at 12 weeks.