Background: Body mass index (BMI), waist circumference (WC) and waist-hip ratio (WHR) are all simple anthropometric tools used to categorize obesity status. This study aimed to determine associations between different anthropometric indices and the attainment of therapeutic lipid goals in patients with atherosclerotic cardiovascular disease (CVD) undergoing secondary prevention. Methods: Between 2010 and 2014, this multi-center study enrolled 5718 patients undergoing secondary prevention for CVD. At study enrollment, total cholesterol, high-density lipoprotein protein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C) and triglyceride (TG)were recorded. This cross-sectional study analyzed these three anthropometric obesity indices and correlations with achieving therapeutic lipid goals. Results: Among the 5718 patients, multivariate analysis revealed that those with higher BMI orWC tended not to meet their HDL-C and TG therapeutic goals. However, neither BMI norWC showed a relationship with achieving the LDL-C target. The patients with an elevated WHR (≥0.98 for males and ≥0.97 for females) were less likely to achieve all three lipid target values, including LDL-C (p = 0.05), HDL-C (p < 0.001) and TG (p < 0.001). Conclusions: Among Taiwanese patients undergoing secondary prevention for CVD, the higher the WHR the lower the likelihood of achieving the lipid therapeutic goals.