Glyoxalase I and II form a ubiquitous glutathione-dependent pathway for the detoxification of reactive and mutagenic ketoaldehydes. Methylglyoxal produced as spontaneous by-product of glycolysis is probably the main physiological substrate. Consequently, African trypanosomes with their exorbitant glucose turnover were expected to have a most efficient detoxification system. Trypanosoma brucei possesses a trypanothione [bis(glutathionyl)spermidine]-dependent glyoxalase II but lacks a glyoxalase I gene. Methylglyoxal reductase as well as dehydrogenase activities are negligible. However, the concentrations of methylglyoxal and advanced glycation end products in the parasites are similar to those in different mammalian cells and the mechanism of methylglyoxal elimination remains elusive. Glyoxalase II is an abundant protein. Overexpression of the gene as well as RNA interference in bloodstream and procyclic cells did not result in a growth phenotype. Deletion of both alleles in procyclic parasites revealed that the enzyme is not essential at least under culture conditions. Recombinant glyoxalase II hydrolyzed the trypanothione-thioesters of methylglyoxal, glyoxal and 4,5-dioxovalerate, substrates of the classical glyoxalase system, with high efficiency. The absence of a glyoxalase I, however, renders these thioesters unlikely as physiological substrates. Here we show that trypanothione-thioesters can be generated from the respective coenzyme A derivative by transesterification. S-Acetyl- and S-propionyltrypanothione obtained by this spontaneous reaction proved to be excellent substrates of T. brucei glyoxalase II. This offers a function for the parasite glyoxalase II as general trypanothione thioesterase independent of ketoaldehyde detoxification.