Wine produced at low temperature is often considered to have improved sensory qualities. To investigate the effects of temperature on winemaking, the expression patterns during the industrial fermentation process carried out at 13 degrees C and 25 degrees C were compared, and correlated with physiological and biochemical data, including viability, fermentation byproducts and lipid content of the cells. From a total of 535 ORFs that were significantly differentially expressed between the 13 degrees C and 25 degrees C fermentations, two significant transcription programmes were identified. A cold-stress response was expressed at the initial stage of the fermentation, and this was followed by a transcription pattern of upregulated genes concerned with the cell cycle, growth control and maintenance in the middle and late stages of the process at 13 degrees C with respect to 25 degrees C. These expression patterns were correlated with higher cell viability at low temperature. The other relevant transcriptomic difference was that several genes implicated in cytosolic fatty acid synthesis were downregulated, while those involved in mitochondrial short-chain fatty acid synthesis were upregulated in the fermentation process conducted at 13 degrees C with respect to that at 25 degrees C. These transcriptional changes were qualitatively correlated with improved resistance to ethanol and increased production of short-chain (C(4)-C(8)) fatty acids and their corresponding esters at 13 degrees C as compared to 25 degrees C. While this increase of ethyl esters may account in part for the improved sensory quality of wine fermented at 13 degrees C, it is still unclear how the esterification of the short-chain fatty acids takes place. On the basis of its strong upregulation at 13 degrees C, we propose a possible role of IAH1 encoding an esterase/ester synthase in this process.