It is now well established that the GS/GOGAT cycle is the major route for ammonium assimilation in higher plants. However, it has often been argued that other enzymes, such as glutamate dehydrogenase, have the capacity to assimilate ammonium, leading to the hypothesis that alternative ammonium assimilatory pathways could operate under particular physiological conditions. The GDH enzyme is encoded by two distinct genes, GDH1 and GDH2. A third gene, GDH3, potentially encoding GDH has recently been identified by in silico studies performed on Arabidopsis thaliana. In order to precise its function, the metabolic profile of gdh3 knock out mutants were compared to wild type plants using the 1H-NMR technique. 1H-NMR spectra coupled with principal component analysis and partial least square-discriminant analysis were applied to identify changes of the metabolic profiles. These experiments were performed on roots, leaves and stems. In the gdh3 mutant, metabolic variations were observed for carboxylic acids, amino acids and carbohydrates content.