Flax and pumpkin seeds are a rich source of unsaturated fatty acids, antioxidants and fibers, known to have anti-atherogenic and hepatoprotective activities. These effects were evaluated in Wistar rats fed with 1% cholesterol diet. The study was performed on 30 male rats divided into three groups: a control group (CD), CD-chol group fed diet with 1% cholesterol and MS-chol group fed diet enriched with flax and pumpkin seed mixture. In CD-chol group, total cholesterol TC, triacylglycerol TG in plasma and liver, plasma LDL-C, atherogenic index AI and LDL/HDL ratio significantly increased. In MS-chol group lipid parameters decreased significantly, plasma and liver fatty acid composition showed an increase of PUFAs (ALA and LA), and MUFAs (oleic and eicosaenoic acid) and a decrease of SFA (palmitic and stearic acid). In plasma and liver of MS-chol group, malondialdehyde levels decreased and the efficiency of antioxidant defense system was improved compared to CD-chol group. Liver histological sections showed lipid storage in hepatocytes of CD-chol group and an improvement was noted in MS-chol group. Our results suggested that flax and pumpkin seed mixture had anti-atherogenic and hepatoprotective effects which were probably mediated by unsaturated fatty acids present in seed mixture.