The anaerobic stress in tissues of higher plants induces a strong change in sugar, protein and amino acid metabolism. Sugars are rapidly consumed through the anaerobic glycolysis to sustain energy production. The partial protein hydrolysis observed under anoxia is a mechanism by which, the release of free amino acids contributes in maintaining the osmotic potential under stress. Among free amino acids, a particular role is played by glutamic acid, being a precursor of some characteristic compounds of the anaerobic metabolism (alanine, γ-aminobutyric acid and putrescine). The glutamine synthetase/glutamate synthase cycle contributes to ammonia re-assimilation and primary assimilation of nitrate, and produces glutamic acid for the synthesis of the other compounds. Some polypeptides involved in these pathways are expressed under anoxia. The importance of amino acid metabolism in the response to anaerobic stress will be discussed.