Aims. To assess the possible effect of polyphenol-rich olive extracts on lipid metabolism in medaka fish by quantifying the expression of lipogenic and lipolytic genes. Materials and methods. Adult medaka fish were maintained in tanks for five days with five extracts at 0.01% in water, causing obesity through a diet rich in carbohydrates, with a control group maintained in water with a normal diet. The extracts contained polyphenols ranging between 7 and 116 mg/g (oleuropein, hydroxytyrosol) with an antioxidant power of 2–13 mmol of 2,4,6-tri(2-pyridyl)-1,3,5-triazine/100 g. After five days, the fish were sacrificed and the hepatic mRNA and its complementary DNA were extracted by reverse transcription. Complementary DNAs were quantified for three lipolytic and three lipogenic genes by real-time PCR. The relative gene expression was calculated from the amplification curves in reference to the control group. Results. The expression of genes involved in lipolysis, including peroxisome proliferator-activated receptor-±, acyl-CoA oxidase 1, and carnitine palmitoyltransferase 1, were clearly decreased in fish subjected to an obesogenic diet, and this situation could not be reversed in fish maintained with polyphenol-rich extracts. In contrast, lipogenic fatty acid synthase, acetyl-CoA carboxylase 1, and sterol regulatory element-binding protein 1 genes increased considerably with the obesogenic diet and reverted to the normal state with the olive extracts. The effect was not dependent on the total polyphenol content, the specific oleuropein or hydroxytyrosol concentration, or the antioxidant power, suggesting a synergistic effect. Conclusion. Olive polyphenols, acting as anti-lipogenic agents, have a positive effect on lipid metabolism, but their mechanism in each gene is different according to the extract, which supports synergistic mechanisms with the different proportions of polyphenols and accompanying phytochemicals in each extract.