Quality of cold stored peach [Prunus persica (L.) Batsch] is negatively affected by woolliness, a consequence of incomplete cell wall solubilization. Low transcript abundance of genes encoding proteins associated with endomembrane transport and cell wall metabolism in woolly fruit has been implicated in the process of woolliness development. In order to test this hypothesis, differential expression of genes involved in transport and cell wall metabolism were studied during ripening of peach cultivars Chimarrita (susceptible to woolliness) and Granada (not susceptible to woolliness), previously stored under cold and controlled atmosphere conditions. Unexpectedly, transcripts of endomembrane transport and cell wall metabolism associated genes had high relative accumulation in woolly ‘Chimarrita’ fruit. Although woolliness tolerant ‘Granada’ peach developed similar up-regulation, its transcript abundance was lower than ‘Chimarrita’. Results presented here suggest that woolliness prevention in peach is not entirely dependent on the up-regulation of this group of genes.