Purpose To determine whether metabolite changes at cellular level occur in vitreous and lateral geniculate body (LGB) in patients with glaucoma by magnetic resonance spectroscopy (MRS). Methods A total of 29 eyes of 29 patients with glaucoma, no existing ocular pathology and systemic disease (group 1), and 13 eyes of 13 healthy individuals whose routine ophthalmological examinations were normal (group 2) were included in the study. Singlevoxel MRS examination was performed by placing region of interest in vitreous and LGB. Glutamate-glutamine (Glx)/creatin (Cr) ratios and lactate peaks in the vitreous, and the Glx/Cr, N-acetyl aspartate (NAA)/Cr, choline (Cho)/Cr ratios in the ipsilateral area of LGB were evaluated. Results A statistically significant difference was found between the two groups for the Glx/Cr ratio in both the vitreous and LGB (P ¼ 0.0001). There was no statistically significant difference between the two groups for the NAA/Cr, and Cho/Cr ratios in the LGB (P ¼ 0.108). A lactate peak was established in the vitreous of 11 glaucoma patients. Conclusion Determining increased Glx/Cr ratios in both the vitreous and LGB of glaucoma patients, supports the theory of apoptosis in the etiopathogenesis of glaucoma. The MRS method, which can measure biochemical structures and metabolites of tissues, and also shows on a single spectrum, may be a new and noninvasive method for confirming the diagnosis of glaucoma and the role of apoptosis in the etiopathogenesis of glaucoma.