To determine which is the best anthropometric index among body mass index (BMI), waist circumference (WC), waist to hip ratio (WHR) and waist to height ratio (WHtR) in type 2 diabetic patients, we examined the relationship between these indices and cardiovascular risk factors using partial correlation analysis, chi-square test, logistic regression analysis and Receiver Operator Characteristic (ROC) curves. Partial correlation analysis showed that among the 4 obesity indices, WHtR had the highest r values for all the cardiovascular risk factors in both sexes, followed by WC. Chi-square analysis which revealed that an increased WHtR was more strongly associated with hypertension, hypertriglyceridemia (high TG) and low high-density lipoprotein cholesterol (HDL-C) than the other indices. Logistic regression analysis showed that, after controlling for age, the hypertension, high TG and low HDL-C odds ratios of WHtR ≥0.5 were 2.56 (95%CI: 1.24, 5.29), 2.87 (95%CI: 1.43, 5.78), 2.59 (95%CI: 1.03, 6.59) in men and 3.75 (95%CI: 1.75, 8.05), 3.21 (95%CI: 1.52, 6.79), 3.62 (95%CI: 1.43, 9.21) in women, respectively. In ROC analysis, the areas under curve of WHtR were the largest for at least one risk factor in both men and women. These results indicated that WHtR had a higher correlation with cardiovascular risk factors than WC, WHR or BMI in newly diagnosed type 2 diabetes. We proposed the measurement of WHtR as a screening tool for cardiovascular risk factors in this population.