Epicardial fat tissue has unique endocrine and paracrine functions that affect the cardiac autonomic system. Epicardial fat thickness (EFT) and blunted heart rate recovery (HRR) are newly identified cardiovascular risk factors in patients with metabolic syndrome (MS). The objective of this study is to evaluate the association between EFT and HRR in patients with MS. Forty patients with MS and 36 healthy controls were included in the study. Echocardiographic EFT and HRR at 1min after exercise termination (HRR-1) are measured and compared between the two groups. HRR-1 equal to or lower than 18 beats is considered as blunted HRR. EFT was increased (7.2 ± 2 vs. 5.6 ± 1.8 mm; p = 0.001) and HRR-1 was significantly reduced in patients with MS compared to control group (21 ± 8 vs. 26 ± 9; p = 0.006). Among the MS patients, subjects with blunted HRR had increased EFT compared to patients without blunted HRR (8.5 ± 2.0 vs. 5.9 ± 1.1 mm, p < 0.001). In multivariate analysis, EFT was the only independent predictor of blunted HRR in patients with MS (95% confidence interval = 1.42-3.87, OR = 2.34, p = 0.001). Furthermore, EFT of equal to or thicker than 5.5 mm was associated with the blunted HRR with 84% sensitivity and 52% specificity (ROC area under curve: 0.84, 95% confidence interval = 0.70-0.96, p < 0.001). In conclusion, EFT is an independent predictor of blunted HRR, a novel cardiovascular risk factor, in patients with MS.