Bai Ku Yao is an isolated subgroup of the Yao minority in China. Little is known about dyslipidemia in this population. The aim of this study was to compare the effects of demography, diet, and lifestyle on serum lipid levels between the Bai Ku Yao and Han populations. A total of 1,170 subjects of Bai Ku Yao and 1,173 subjects of Han Chinese aged 15-89 years were surveyed by a stratified randomized cluster sampling. The levels of total cholesterol, high density lipoprotein cholesterol, low density lipoprotein cholesterol, apolipoprotein A-I (apoA-I), and apoB were significantly lower in Bai Ku Yao than in Han. Physical activity level and total dietary fiber intake were higher, whereas body mass index (BMI), waist circumference, total energy intake, and total fat intake were lower in Bai Ku Yao than in Han. Hyperlipidemia was positively correlated with BMI, waist circumference, and total energy and total fat intakes and negatively associated with physical activity level and total dietary fiber intake in both populations, but it was positively associated with age and alcohol consumption only in Han. The differences in the lipid profiles between the two ethnic groups were associated with different dietary habits, lifestyle choices, and levels of physical activities.