A fatty acid hydroperoxide lyase from soybean seeds (Glycine max var. Williams) has been partially purified by differential centrifugation, ion-exchange chromatography, and gel filtration. The enzyme preparation, which is free of cis-3:trans-2-enal isomerase, has an optimun pH in the range 6-7. The lyase cleaves the 13-hydroperoxides of linoleic and linolenic acids to form the volatile aldehydes hexanal and cis-3-hexenal, respectively. In both case the ω-oxo carboxylic acid 12-oxo-cis-9-dodecenoic acid is also formed. The enzyme does not act on 9-hydroperoxides of these acids. The activity of hydroperoxide lyase was followed for 6 days of germination and found to increase constantly. Lipoxygenase activity (L-2 + L-3) also increased, as did the level of fluorescence in the phospholipids extracted. These facts suggest that lipoxygenase and hydroperoxide lyase may be involved in the formation of fluorescent substances. © 1990, American Chemical Society. All rights reserved.