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Photorespiration is a metabolic process that removes toxic 2-phosphoglycolate produced by the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase. It is essential for plant growth under ambient air, and it can play an important role under stress conditions that reduce CO₂ entry into the leaf thus enhancing photorespiration. The aim of the study was to determine the impact of photorespiration on <i>Arabidopsis thaliana</i> leaf amino acid metabolism under low atmospheric CO₂ concentrations. To achieve this, wild-type plants and photorespiratory glycolate oxidase (<i>gox</i>) mutants were given either short-term (4 h) or long-term (1 to 8 d) low atmospheric CO₂ concentration treatments and leaf amino acid levels were measured and analyzed. Low CO₂ treatments rapidly decreased net CO₂ assimilation rate and triggered a broad reconfiguration of soluble amino acids. The most significant changes involved photorespiratory Gly and Ser, aromatic and branched-chain amino acids as well as Ala, Asp, Asn, Arg, GABA and homoSer. While the Gly/Ser ratio increased in all Arabidopsis lines between air and low CO₂ conditions, low CO₂ conditions led to a higher increase in both Gly and Ser contents in <i>gox1</i> and <i>gox2.2</i> mutants when compared to wild-type and <i>gox2.1</i> plants. Results are discussed with respect to potential limiting enzymatic steps with a special emphasis on photorespiratory aminotransferase activities and the complexity of photorespiration.