Background and Objective: The relationship between diabetes mellitus and increased risk of cardiovascular diseases has been demonstrated. The aim of this study was to determine the fatty acid profile of epicardial adipose tissue in diabetic and non-diabetic patients with cardiovascular disease. Methods: In this study, 28 diabetic and 40 nondiabetic patients were evaluated. The epicardial adipose tissue and blood samples of patients were collected during surgery. Nonesterified fatty acids and phospholipids were measured by the thin layer chromatography and gas chromatography. Results: Saturated free fatty acids (12: 0) level was higher in diabetic patients compared to nondiabetic patients (P=0.038), while saturated free fatty acids (16: 0) was significantly lower in diabetics (P=0.011). Unsaturated fatty acid (20: 3n-9) was higher in nondiabetics compared to diabetics (P=0.015). There was a significant decrease in level of monounsaturated fatty acids in diabetic patients. The epicardial adipose tissue of diabetics showed a significant increase in free fatty acid (18: 0) and conjugated linoleic acid levels, while there was a significant decrease in the level of free fatty acid (18: 1n-11). Level of epicardial omega-3 free fatty acid (20: 5 n-3) and 22: 6 n-3 was significantly reduced in these patients. Conclusion: Differences in the serum free fatty acid profile of the two groups may be due to differences in their diet, while changes in the fatty acid composition of epicardial adipose tissue in these two groups could be due to impaired metabolism of fatty acids such as uptake, movement and androgen synthesis as a result of diabetes. These changes increase the risk of developing atherosclerosis in diabetic patients.