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The study explored the effects of trans-fatty acids (TFA) on the antioxidant system and ATPase levels in liver and kidney of rats. Forty-eight healthy male Wistar rats of SPF grade were randomly divided into four groups according to their weight, which were control group, low dose TFA group, medium dose TFA group and high dose TFA group. The control group received 0.2 ml/kg corn oil once a day, while the TFA low dose group, TFA medium dose group and TFA high dose group respectively received 50, 100, 150 mg/kg/day trans-fatty acids, for 12 consecutive weeks. The tested chemicals were given by gavage. The activities of superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), ATPase and the content of malondialdehyde (MDA) in the liver and kidney were determined. Compared with the control group, trans-fatty acids intake caused significant increase of MDA but reduction of the activities of SOD and GSH-Px (P<0.05) in liver and kidney, meanwhile, trans-fatty acids exposure caused a significant reduction of the activities of Na+ K+-ATPase, Mg2+-ATPase and Ca2+-ATPase (P<0.05) in liver and kidney. The results suggested that trans-fatty acid exposure can impair the antioxidant system and reduce the ATPase activity in liver and kidney of rats.