Due to their health-promoting effects green tea catechins have gained a keen interest in recent years in the context of bodyweight reduction treatments and alleviation of inflammatory diseases. This study was designed to evaluate the impact of native and thermally modified catechins (TMC) on the body weight gain, fatty acid profile in subcutaneous adipose tissue and the activity of the enzymes involved in lipid metabolism regulation: AMP-dependent protein kinase (AMPK) and acetyl-CoA carboxylase (ACC) in apoE-deficient mice maintained on a high-fat diet. We observed that TMC decreased bodyweight gain as compared to the control group. Furthermore, TMC increased AMPK activity and reduced ACC activity in the metabolically important tissues: intestine, liver and subcutaneous adipose tissue and affected adipose tissue fatty acid composition. Native catechins produced less pronounced effects. These results suggest that TMC down-regulate endogenous fatty acid synthesis, which should be taken into account in dietary applications of catechins.