Background: Employees are considered as an at-risk group for obesity and its adverse outcomes, particularly cardiovascular diseases (CVD). The present study was conducted to assess the correlation of obesity indices with CVD risk factors among a group of medical university employees in Zahedan city, southeast of Iran. Methods: This cross-sectional study recruited 211 healthy employees of Zahedan University of Medical Sciences during October 2015. Obesity indices including body mass index (BMI), waist circumference (WC), waist to hip ratio (WHpR), and waist to height ratio (WHtR) were measured in accordance to the standard criteria. Fasting blood glucose (FBG), blood lipids, and blood pressure were also measured. Results: Women had significantly higher values of weight, WC, WHpR, and FBG than men (P < 0.05). Bivariate analysis showed that those with BMI, WC, or WHtR higher than the cut-off-point levels had significantly higher serum levels of blood parameters and blood pressure compared to normal participants, respectively. BMI and WC had significant positive correlation with all parameters except with high density lipoprotein-cholesterol; these correlations were slightly stronger for WC compared to BMI. However, the correlation of WHpR and WHtR with metabolic parameters was weak. Conclusions: BMI and WC had an almost moderate correlation with CVD risk factors among the participants. Therefore, using WC along with BMI is suggested as the preferred method for assessment of CVD risk factors.