Seventeen wk old male obese Zucker rats were given 0.4% (w/w) conjugated linoleic acid (CLA) isomers for 8 wk to determine effects of specific isomers on multiple eicosanoids in obesity. Liquid-chromatography-mass spectrometry analysis showed that compared to controls, those given t10,c12 CLA had increased liver leukotriene B4 levels, while immunoblotting revealed that rats given either t10,c12 or c9,t11 CLA had lower liver cyclooxygenase-2. In kidney, compared to c9,t11 CLA or controls, t10,c12 CLA increased cyclooxygenase-1, 6-keto-prostaglandin F2α and thromboxane B2 and inhibited the in vitro production of 13-hydroxyoctadecadienoic acid and 5-, 8-, 12- and 15-hydroxyeicosatetraenoic acid. In lean compared to fa/fa rats, endogenous levels and in vitro production of liver and kidney 9- and 13-hydroxyoctadecadienoic acid were elevated. Previous investigations on these tissues revealed that t10,c12 CLA reduced hepatic steatosis, but increased renal damage. How these changes in eicosanoids in response to t10,c12 CLA relate to the previous findings remains to be elucidated.