The biosynthesis of R-octane-1,3-diol and R-5(Z)-octene-1,3-diol, two natural antimicrobial agents in apples and pears, was investigated in stored apples after application of [9,10,12,13-3H]linoleic acid, [9,10,12,13,15,16-3H]linolenic acid, [1-14C]linoleic acid, [U-14C]oleic acid, lipoxygenase-derived metabolites of [9,10,12,13-3H]linoleic acid, 13C18-labeled linoleic acid hydroperoxides, and 2H-labeled octanol derivatives. Analysis of the products and quantification of incorporation and labeling pattern were achieved by high-performance liquid chromatography-radiodetection, capillary gas chromatography (GC)-isotope ratio mass spectrometry, and GC-mass spectrometry analysis. Almost all the applied precursors were partly transformed into R-octane-1,3-diol. Linoleic acid derivatives, still containing the 12,13 cis double bond, and octanol derivatives oxy-functionalized at carbon 3 were the most efficient precursors of the 1,3-diol. The data imply that R-octane-1,3-diol is generated in stored apples in the course of the beta-oxidation from R-3-hydroxy-octanoyl-SCoA originating from 2-cis-octenoyl-SCoA by enoyl-CoA hydratase. In an analogous fashion, R-5(Z)-octene-1,3-diol is formed from the unsaturated intermediate.