Aspartic acid, glutamic acid and alanine were measured in the cochlear nucleus after lesioning the auditory nerve by cochlear ablation. Ultrastructural analysis of the cochlear nucleus showed that most primary auditory terminals were degenerating one day after cochlear ablation; the terminals were enlarged and the number of synaptic vesicles was reduced. Primary auditory terminals were virtually gone three days after cochlear ablation. Aspartic acid decreased after cochlear ablation in parallel with the morphological degeneration of the primary auditory terminals. The level of total aspartic acid in the cochlear nucleus had decreased more than 8% one day after cochlear ablation and more than 30% after two days, and remained at this level up to 28 days. Glutamic acid also decreased in the cochlear nucleus after cochlear ablation but not in parallel with the morphological degeneration of the primary auditory terminals. Following a slight increase one day after cochlear ablation, total glutamic acid decreased about 10% after two days and continued to decrease slowly through to day 28. Alanine dropped slowly after cochlear ablation and not in parallel with the degeneration of the primary terminals. Levels of other amino acids measured were unchanged or had increased two days after cochlear ablation. Aspartic acid and glutamic acid did not decrease in the superficial layers of the dorsal cochlear nucleus, an area receiving little or no primary innervation.