The aim of this study was to investigate the effects of fermented milk contains bifidobacteria on plasma lipid levels and selected genes in hypercholesterolemic rats. Effects of Bifidobacterium longum BB536 with prebiotics on body weight of rats, level of bile acids and selected genes were studied. Sprague-Dawley rats were randomly divided into groups. Negative control group received standard diet, positive control group received high-cholesterol diet, and intervention groups received high-cholesterol diet added with fermented milk contains Bifidobacterium longum BB536 in presences of prebiotics. After 8 weeks, body weight, level of bile acids were measured and low density lipoprotein receptor and 3-hydroxy-3-methylglutaryl-coenzyme A reductase were investigated in rats’ liver using quantitative real-time polymerase chain reaction. Fermented milk contains Bifidobacterium longum BB536 increased weight of rats and level of bile acids over 8 weeks of intervention. Low density lipoprotein receptor gene level was increased significantly in fermented milk treated rats compared to positive control. Whereas, 3-hydroxy-3methylglutaryl-coenzyme. A reductase gene level was decreased significantly in fermented milk treated compared to positive control. The present study showed that fermented milk contains Bifidobacterium longum BB536 effectively regulated the expression of low-density lipoprotein receptor and 3-hydroxy-3-methylglutaryl-coenzyme A reductase genes influencing the cholesterol metabolism in liver cells.