Introduction: Non-alcoholic fatty liver disease (NAFLD) often occurs together with obesity. Body mass index (BMI) and waist circumference (WC) are two important physical parameters of obesity. Here we analyzed in a Chinese population the statistical relationship between NAFLD and these two obese parameters. Methods: Data were collected retrospectively from the Taichung Verteran General Hospital during a three-year period from January 2007 to December 2009. Exclusion criteria included large consumption of alcohol and chronic hepatitis (B and C). Patients first went through liver ultrasound scanning and then were assigned to either the normal or fatty liver group. Patients were also subgrouped as either overweight/obesity (BMI≧25 mg/m2) or normal weight; central obesity (waist circumference ≧ 90 cm for men and ≧ 80 cm for women) or normal. The statistical association with NAFLD was then compared for each subgroup. Results: A total of 916 patients (24.3%) were classified into the fatty liver group and 2868 patients (75.8%) were classified into the normal group. The ratios of overweight/obesity (59.0% vs. 49.4%, P=0.001) and central obesity (18.4% vs. 15.7%, P=0.006) were significantly higher in the fatty liver group compared with the normal. The positive association with NAFLD was significant in overweight/obesity (OR 1.46, 95% CI 1.33 to 1.73), but insignificant in central obesity (OR 1.29, 95% CI 0.83 to 2.03). After further stratification, significant positive association was found in patients with both higher BMI and WC (OR 2.09, 95% CI 1.39 to 3.80) and higher BMI but normal WC (OR 1.42, 95% CI 1.17 to 1.73). But such association was not found in those with higher WC but normal BMI (OR 1.05, 95% CI 0.60 to 1.84). Conclusion: BMI, and not WC, had a strong positive association with NAFLD. Patients with higher BMI and higher WC had additional risk for NAFLD.