A microarray containing over 10,000 gene fragments was used to link changes in gene expression with changes in aroma biosynthesis in ripening apple (Malus ×domestica Borkh). The microarray was probed with fluorescent-tagged cDNA derived from RNA extracted from `Jonagold' apple skin and cortex tissue representing eight distinct physiological stages spanning 70 days during ripening and senescence. The ripening stages, in chronological order, were: 1) early preclimacteric; 2) late preclimacteric and onset of trace ester biosynthesis; 3) onset of the autocatalytic ethylene and rapidly increasing ester biosynthesis; 4) half-maximal ester biosynthesis and engagement of the respiratory climacteric; 5) near maximal ester biosynthesis, peak in respiratory activity, and the onset of rapid tissue softening; 6) maximal ester biosynthesis prior to its decline, the conclusion of the respiratory climacteric, and the completion of tissue softening; 7) midpoint in the decline in ester biosynthesis and maximal ethylene biosynthesis; and 8) postclimacteric minimum in ester production. Patterns in gene expression reflecting the rise and fall in ester formation were found in some putative genes for beta-oxidation (acyl-CoA oxidase, enoyl-CoA hydratase, and acetyl-CoA acetyl transferase), ester formation (aminotransferase, alcohol dehydrogenase, and alcohol acyl transferase), and fatty acid oxidation (lipoxygenase), but not fatty acid biosynthetic genes. A marked decline coinciding with the onset of ester production was detected in several putative genes for ADH.