Raphani Semen (RS) has been used to treat digestive disorders in Korean oriental medicine. The hypolipemic and anti-obese effects of the aqueous extracts of RS in mice provided with high fat diet (HFD) were evaluated. HFD caused increased T-Chol, triglyceride, and LDL, and decreased HDL levels. Mice fed HFD exhibited signs of obesity including increased body weight, fat weight, and serum leptin level, and decreased serum adiponectin level. Histopathological analysis revealed that the mean diameter of adipocytes was increased by HFD supply. However, these increases in the hyperlipemia and obesity indices were attenuated by RS treatment in a dose-dependent manner, and similar effects were detected in mice treated with equal dosages (250 mg/kg) of metformin and RS. These results indicate that the aqueous extracts of RS warrant further development as a protective agent for the treatment of diet-induced metabolic syndrome.