Cholesterol-lowering effects of tomato pomace, seed oil and defatted seed were studied. ► Defatted seed lower total and LDL plasma cholesterol. ► The pomace, oil and defatted seed reduced hepatic cholesterol. ► Fecal lipid, bile acid, and cholesterol were increased by defatted seed feeding. ► Expressions of lipid metabolism genes support mechanism of bile acid pool depletion