Tomato is sensitive to cold during vegetative growth, fruit set, development, and ripening. We have characterized the effect of cold stress (6xC for up to 48 h) on the transcriptome of Micro-Tom tomato fruits during ripening by subtractive PCR. The cold stress caused modifications in gene expression of housekeeping genes. From a total of 38 genes up-regulated by cold, only one clone - a dehydrin homologue - was related to previously identified cold-stress genes. Phylogenetic analysis showed its clustering with other cold-induced dehydrins, and increased distances from dehydrins activated by abscisic acid. Quantitative expression analysis of tomato dehydrin showed it was activated by cold treatment in leaves and fruits. As dehydrin is a member of the Sl-CBF1 regulon from tomato, we analyzed the cold-responsive transcription factor Sl-CBF1 in mature leaves and ripening fruits stored at 6xC. Leaves of Micro-Tom showed high basal levels of the transcription factor Sl-CBF1, compared to fruits. Cold treatment caused increased levels of Sl-CBF1 expression in leaves but not in fruits of Micro-Tom and Demisem (a commercial cultivar). Tomato dehydrin can be used as a transcriptional marker of cold stress in leaves and ripening fruits. However, our results indicate that the cold response activation of dehydrin gene in tomato fruits is the consequence of an alternative pathway, different from the Sl-CBF1 regulon.