Hypercholesterolemia and hypertriglyceridemia are major risk factors that accelerate the incidence of atherosclerosis and coronary artery diseases. Therefore, the present study was conducted to evaluate the hypolipidemic effect of widely known traditional medicinal herbs and omega-3 FA in experimental hypercholesterolemia induced by Triton WR-1339. Experimental hypercholesterolemic rats were administered mushroom, chrysin, curcumin and omega-3 for 2 weeks. Hypercholesterolemic rats showed an increase in serum levels of lipid profiles and hepatic enzymes. Hypercholesterolemic rats showed an increase in malondialdehyde (MDA) levels and a decrease in both serum levels and mRNA expression of catalase, superoxide dismutase (SOD) and glutathione reducatse. Moreover, hypercholesterolemic rats showed hepatic down regulation in the expression of genes related to fatty acids oxidation such as acyl CoA oxidase (ACO) and synthetase (ACS), together with carnityl palmityl transferase-1 (CPT-1) and peroxisome proliferator activator receptor-α (PPAR-α). Administration of mushroom, chrysin, curcumin and omega-3 to hypercholesterolemic rats for 2 weeks up-regulated significantly the down regulated genes. In contrast, expression of genes related to fatty acids biosynthesis and cholesterol metabolism were increased in hypercholesterolemic rats compared to control group. Herbal medications and omega-3 administration down regulated genes of fatty acids biosynthesis and cholesterol metabolism to normal expression. At cellular levels, hyperlipidemia induced fatty droplets accumulation, necrosis and presence of apoptotic hepatocytes together with leukocytic infiltration in necrotic area that are ameliorated and normalized after administration of herbs and omega-3. In conclusion, the current findings indicated that flavonoids (mushroom, chrysin, curcumin) and omega-3 possess antihypercholesterolemic effects at biochemical, molecular and histopathological levels and are useful in treatment of hypercholesterolemia with lower side effects compared with synthetic hypolipidemic drugs.