We extracted the protein fraction (QP) from quinoa seeds. Mice were fed on 0.5% cholesterol diet, containing 0%, 2.5% and 5.0% of QP (control, QP 2.5% and QP 5.0%, respectively) for 4 weeks. Neither supplemental QP diet produced a difference in food intake and body weight gain. The QP supplementation significantly prevented the increase in plasma and liver total cholesterol levels. Fecal weight and excretion of bile acids in the QP groups was significantly higher than in the control group. QP showed bile acid-binding activity in vitro. Expression of mRNA of 3-hydroxy-3-methylglutaryl coenzyme A reductase in the liver, a key enzyme for cholesterol biosynthesis, was suppressed by the QP diet, whereas the expression of cholesterol-7α-hydroxylase, a cholesterol catabolic enzyme, was found to be stimulated. These results suggest that the prevention of increases in plasma and liver cholesterol levels in mice fed the QP diet can be ascribed to the inhibition of the re-absorption of bile acids in the small intestine and control of cholesterol synthesis and catabolism.