This study examines how obesity is distributed across socio-economic gradients, and investigates the relationship between obesity and obesity-related chronic diseases in rural Yunnan province of China. The study design is a cross-sectional community survey. A cross-sectional survey was conducted in three rural areas of Yunnan province between 2008 and 2010, among 10,007 consenting individuals aged ≥18 years. Information on demographic characteristics, smoking and drinking habits, self-reported stroke and ischemic heart disease (IHD), and family history of obesity-related chronic diseases was obtained using a standard questionnaire. Fasting blood sugar level, blood pressure, height, weight, and waist and hip circumference measurements were recorded for each individual. The age-standardized prevalence of obesity and central obesity was 8.8% and 46.0% among the study populations, respectively. Obesity and central obesity were more common in females than in males. After adjusting for age, sex, and current smoking and drinking status, individuals who belonged to an ethnic minority group had a lower probability of being both obese and centrally obese. Educational level was found to be negatively associated with the prevalence of obesity, and yearly household income was found to be positively associated with prevalence of central obesity. The results of logistic regression analysis indicated that obese and centrally obese people were more likely to suffer from diabetes, hypertension, and stoke. A positive association of IHD was only found in centrally obese people. In order to reduce the obesity epidemic in rural southwest China, effective interventions must address socio-economic factors. Reducing obesity has a profound impact on the reduction of morbidity associated with cardiovascular diseases and diabetes. Copyright © 2013 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.