Potato tubers under cold storage accumulate sugar, which causes browning of chips and French fries during frying. After cold storage, tubers often need to be treated under warm conditions to reduce the sugar content before frying. The gene expression profiles in these stored tubers are still largely unknown although there have been excellent reports on the molecular and physiological characteristics of cold-stored tubers. In this study, we sequenced and analyzed expressed sequence tags (ESTs) of potato tubers under different temperatures, as part of the Canadian Potato Genome Project (www.cpgp.ca). Greenhouse-grown tubers of 'Shepody' were used to establish cDNA libraries for EST sequencing. The cold-stored-tuber EST library (4°C, 3 months) was a normalized library, and the reconditioned-tuber EST library (4°C for 3 months, then reconditioned at 21°C for 3 days) was a standard library. ESTs were processed, clustered and assembled into high quality contiguous and unique sequences. Approximately 5,000 high quality ESTs were generated from each library. These ESTs and unigenes provide useful resources for studying the metabolic regulation and gene discovery in stored potato tubers.