In organisms, methylglyoxal is formed as a side-product of several metabolic pathways. Methylglyoxal mainly arises as side products of glycolysis involving glyceraldehyde-3-phosphate and dihydroxyacetone phosphate.  It is also thought to arise via the degradation of acetone and threonine. Illustrative of the myriad pathways to MGO, aristolochic acid caused 12-fold increase of methylglyoxal from 18 to 231 μg/mg of kidney protein in poisoned mice. It may form from 3-aminoacetone, which is an intermediate of threonine catabolism, as well as through lipid peroxidation. However, the most important source is glycolysis. Here, methylglyoxal arises from nonenzymatic phosphate elimination from glyceraldehyde phosphate and dihydroxyacetone phosphate (DHAP), two intermediates of glycolysis. This conversion is the basis of a potential biotechnological route to the commodity chemical 1,2-propanediol.
Since methylglyoxal is highly cytotoxic, several detoxification mechanisms have evolved. One of these is the glyoxalase system. Methylglyoxal is detoxified by glutathione. Glutathione reacts with methylglyoxal to give a hemithioacetal, which converted into S--lactoyl-glutathione by glyoxalase I. This thioester is hydrolyzed to -lactate by glyoxalase II.