Mandarin sensory acceptability deteriorates rapidly after harvest. To gain a better understanding of the molecular processes that occur in 'Mor' mandarin flesh and contribute to flavor deterioration during storage, we performed genome-wide transcriptional profiling analysis using the Affymetrix Citrus GeneChip. Out of 30,171 probe sets representing citrus transcripts on the microarray, expression of 1,139 probe sets was significantly (q ≤ 0.01) altered by factors of at least 4 after 6 weeks of cold storage at 5 °C, of which 745 (65%) were downregulated and 394 (35%) upregulated. Overall, storage led to expression arrest of general cellular and metabolic activity, but enhanced lipid and amino acid catabolism, most probably to form substrates for the tricarboxylic acid (TCA) cycle and energy production. In addition, storage enhanced gene expression of pyruvate decarboxylase (PDC), a key enzyme in anaerobic respiration and the ethanol fermentation pathway. Taken together, we propose that induction of amino acids and fatty acids degradation leads to accumulation of volatiles involved in formation of "fruity" (overripe) and "musty" aromas, respectively, whereas induction of ethanol fermentation metabolism leads to formation of "alcohol" flavor, all of which generate off-flavors after harvest.