Objective To detect the serum lipids levels in the subjects aged 40 years and over in the Guangxi Bai Ku Yao population. Methods A total of 485 subjects of Bai Ku Yao and 501 Han people aged 40 years and over were surveyed by cluster sampling methods. Informations on demography, diet and lifestyle were collected by standard questionnaires. Blood pressure, height,weight, waist circumference, serum lipids and apolipoproteins (apo) were measured, and body mass index (BMI) was calculated. Results Education level, height, weight, BMI, waist circumference,blood pressure levels, hypertensive prevalence, and the intakes of total energy, total fat, total protein, dietary cholesterol, and salt were higher in Han than in Bai Ku Yao (P<0.05 or P<0.01),whereas physical activity level, and the intakes of carbohydrate, vegetal protein, and total dietary fiber were higher in Bai Ku Yao than in Han (all P<0.001). The serum levels of total cholesterol,high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, apo A1, and apo B were significantly lower in Bai Ku Yao than in Han [(4. 43±0. 90)vs. (4.96±1.04)mmol/L, P<0. 001;(1.73±0. 42) vs. (2.01±0. 49) mmol/L, P<0. 001;(2. 62±0. 75) vs. (2. 72±0. 78)mmol/L, P<0. 05;(1. 36±0. 33) vs. (1. 48±0. 24)g/L, P<0. 001;and (0. 86±0.23) vs. (0. 95±0. 22)g/L,P<0. 001 ;respectively]. There were no significant differences in serum triglyceride level and the ratio of apo Al over apo B between the two ethnic groups (P>0. 05). Conclusions There are significant differences in lipids levels and the risk factors between Bai Ku Yao and Han populations, which might result from different dietary habits, life styles, and physical activities.