Recent behavioural and neurophysiological studies suggest that the hippocampus uses vestibular information, along with information from other sensory systems, to accomplish its spatial computational processing. By contrast, there is a dearth of neurochemical data on the interactions between the vestibular system and hippocampus. The aim of the present study was to examine levels of glutamine, glutamate, gamma-amino-butyric acid (GABA), glycine, serine, threonine and taurine in the CA1, CA2, CA3 and dentate gyrus (DG) subregions of the hippocampus at 10 hs following UVD in guinea pig, using high-performance liquid chromatography (HPLC) with electrochemical detection (ECD). Glutamine levels were not significantly different between the UVD and control conditions, except in the bilateral DG where they were significantly lower (p < 0.05). However, no significant differences in glutamate levels were observed. Although there were no significant differences in GABA levels in the DG, CA1 and CA2 regions following UVD, there was a significant increase in GABA levels in the contralateral CA3 region in the sham group compared to intact anesthetic controls. Glycine levels were significantly higher in the contralateral DG and ipsilateral CA1 in the sham groups compared to intact anesthetic controls (p < 0.05). However, in contralateral CA2 and ipsilateral CA3, glycine levels were significantly higher for both the sham and UVD groups compared to anesthetic controls (p < 0.05). Threonine levels were not significantly different in CA1; however, in ipsilateral DG and ipsilateral CA3, they were significantly higher in the sham groups compared to anesthetic controls and the UVD groups (p < 0.05). In ipsilateral CA2, threonine levels were significantly higher in the UVD group compared to anesthetic controls (p < 0.05). Taurine levels did not differ significantly in the DG, CA1 or CA3 following UVD; however, they were significantly higher in ipsilateral CA2 following UVD (p < 0.05). Finally, serine levels were not significantly different in any area of the hippocampus following UVD or sham surgery. This study provides the first data on amino acid levels in the hippocampus following UVD and sham temporal bone surgery and suggests that peripheral vestibular damage may particularly affect glutamine, glycine, threonine and taurine levels in various subregions of the hippocampus.