We examined low temperature-induced protein profile alterations in the Antarctic alga Chaetoceros neogracile using a proteomic approach. Chaetoceros neogracile was cultured at 4 degree C and then cooled to 0 degree C, and the resultant cold-induced alterations in protein expression patterns were analyzed by two-dimensional gel electrophoresis. Of the approximately 150 protein spots detected by Coomassie staining, we identified 15 with a greater than two-fold change in amount. Of these, ten proteins were up-regulated and five were down-regulated after cold exposure. Three cellular protein quality control proteins, such as chaperone protein DnaK, chaperone ClpB, and 26S protease regulatory subunit 6B homolog were prominently increased, whereas chaperone protein HtpG was decreased in response to cold stress. Moreover, changes in enzyme activity and isozyme profiles for superoxide dismutase, glutathione reductase, and glutathione S-transferase were also detected in the gel, using an enzyme activity staining method. These alterations in protein expression and antioxidant enzyme activity may be related to survival mechanisms of C. neogracile at low temperatures.