We investigated metabolite levels during the progression of pathology in McGill-R-Thy1-APP rats, a transgenic animal model of Alzheimer's disease, and in healthy age-matched controls. Rats were subjected to in vivo 1 H magnetic resonance spectroscopy (MRS) of the dorsal hippocampus at age 3, 9 and 12 months and of frontal cortex at 9 and 12 months. At 3 months, a stage in which only Ab oligomers are present, lower glutamate, myo-inositol and total choline content were apparent in McGill-R-Thy1-APP rats. At age 9 months, lower levels of glutamate, GABA, N-acetylaspartate and total choline and elevated myo-inositol and taurine were found in dorsal hippocampus, whereas lower levels of glutamate, GABA, glutamine and N-acetylaspartate were found in frontal cortex.At age 12 months, only the taurine level was significantly different in dorsal hippocampus, whereas taurine, myo-inositol, N-acetylaspartate and total creatine levels were significantly higher in frontal cortex. McGill-R-Thy1-APP rats did not show the same changes in metabolite levels with age as displayed in the controls, and overall, prominent and complex metabolite differences were evident in this transgenic rat model of Alzheimer's disease. The findings also demonstrate that in vivo 1 H MRS is a powerful tool to investigate diseaserelated metabolite changes in the brain. Keywords: biomarkers, GABA, glutamate, metabolism, N-acetylaspartate, transgenic rats. Alzheimer's disease (AD) is a progressive neurodegenerative disease and the most common cause of dementia in the elderly. It is characterized by accumulation of extracellular plaques containing aggregated amyloid b (Ab) peptides and intracellular neurofibrillary tangles composed of hyperphosphorylated tau proteins. In addition, regional loss of neurons and synapses, progressive cognitive decline and regional hypometabolism occurs (Mosconi 2005; SerranoPozo et al. 2011). Emerging evidence also suggest that, intraneuronal Ab oligomers may contribute substantially to AD disease progression (Haass and Selkoe 2007).There is no definite biomarker for the diagnosis of AD, which motivates the search for neuroimaging markers that may facilitate early detection of the disease. Using 1 H magnetic resonance spectroscopy (MRS), the regional concentration of low-molecular-weight metabolites can be measured non-invasively and provides insight into neurochemical processes of normal and pathological conditions in vivo. Performing 1 H MRS of patients with AD has revealed a consistent pattern of decreased levels of Nacetylaspartate (NAA) or NAA/total creatine (tCr) and increased myo-inositol (mIns) or mIns/tCr (Kantarci et al. 2003;Shiino et al. 2012). NAA is synthesised in neurons (Wiame et al. 2010) Abbreviations used: AD, Alzheimer's disease; APP, amyloid precursor protein; Ab, amyloid beta; CMR glc , cerebral metabolic rate of glucose; CRLB, Cramer-Rao lower bounds; DH, dorsal hippocampus; FCX, frontal cortex; GS, glutamine synthetase; mIns, myo-inositol; MRI, magnetic resonance imaging; MRS, magnetic resona...