Background and Objective: Obesity and metabolic syndrome are major risk factors for cardiovascular diseases. This study compared heart rate variability (HRV) indices, structural and functional echocardiographic variables, and the metabolic syndrome‑based insulin resistance index (METS-IR) in healthy obese men and obese men with metabolic syndrome. Materials and Methods: In this comparative cross-sectional study, 44 obese men with no history of cardiac diseases were divided into two groups: healthy obese (n=22) and obese with metabolic syndrome (n=22) based on NCEP ATP III criteria. Anthropometric, metabolic (FBG, TG, HDL, METS-IR), cardiovascular (blood pressure, heart rate), HRV (SDNN, RMSSD, LF/HF) at rest, during exercise, and recovery (by Holter ECG), and echocardiographic (LVM, LVEDV, EF, E/A) variables were measured. Data were analyzed using independent t-test. Results: The obese group with metabolic syndrome showed higher FBG, TG, METS-IR, blood pressure, and heart rate (P-value <0.05) and lower SDNN, RMSSD (except RMSSD_rest with P=0.058), and higher LF/HF ratio at rest, during exercise, and recovery (P-value <0.05). Significant differences were also found in LVM, LVEDV, ventricular wall thickness, EF, and E/A (P-value <0.05). Conclusion: Metabolic syndrome in obese individuals is associated with greater impairment in cardiac autonomic balance, cardiac structure, and function.