Spinal cord injury (SCI) is a complex process that affects not only the spinal cord itself, but also brain metabolism and morphology. We used magnetic resonance spectroscopy (MRS) to study metabolite changes due to injury-induced functional modifications of thalamic nuclei during 2 weeks post-SCI. We used 2 groups of Wistar rats: the 1st group (SCI) underwent balloon compression to create a lesion at the T8-T9 level, while the 2nd group was sham operated. Single-voxel MRS (4.7T, Bruker) was performed one day before and 1, 3, 6 and 15 days after surgery in both groups. Our results show that there was a significant increase (P<0.01) in N-acetylaspartate (NAA) concentration the first day after SCI in the thalamic nuclei region; levels were still significantly elevated, but decreasing, on day 3 post-SCI. Also on day 3, the concentrations of inositol (Ins) (P<0.01), glutamate (Glu) (P<0.01) and creatine (Cr) (P<0.05) were increased in SCI rats. Cr levels were also significantly increased in sham operated animals (P<0.05) 3 days after surgery. On day 6, Ins remained significantly elevated (P<0.01) in the SCI animals. Two weeks after injury all metabolite concentrations in both groups were decreasing to baseline levels, except for Glu which was increasing (P<0.05) 15 days after SCI. Our data indicate that there are several changes in thalamus metabolism after SCI, suggesting pathophysiological alterations caused by impaired transmission between the brain and spinal cord.