Background/aim: The aim of this study was to evaluate the effects of 6-months treatment with exenatide on lipid profile, high sensitivity C-reactive protein (hsCRP), carotid intima media thickness (CIMT), visceral adiposity and non-alcoholic fatty liver disease (NAFLD), which are all important cardiovascular risk factors. Materials and methods: This study included 45 obese patients with type 2 diabetes mellitus (T2DM). The baseline clinical findings, laboratory parameters and ultrasonography findings were recorded. Exenatide twice daily recipe was given to these patients and after 6 months of therapy the same variables were compared. The compared parameters were lipid profiles, hsCRP, aspartat aminotransferase, alanine aminotransferase, gamma-glutamyltransferase, liver craniocaudal diameter, visceral fat volume, subcutaneous fat thickness and CIMT. Liver diameter, visceral fat volume and subcutaneous fat thickness and CIMT were measured with ultrasonography. Results: After therapy, statistically significant improvement were achieved in lipid profile, hsCRP, liver enzymes, body mass index, waist and hip circumferences. Also statistically significant decrease were obtained in liver craniocaudal diameter, subcutaneous fat thickness, visceral fat volume and CIMT. The reduction of CIMT and liver diameter were not correlated with BMI and HbA1c reduction. Conclusion: This study showed improvement in lipid profile and hsCRP levels with exenatide treatment. We also showed decrease in both visceral fat volume and subcutaneous fat thickness. We demonstrated significant decrease in liver enzymes with 2 significant decrease in liver diameter. These findings supports the use of exenatide in patients with NAFLD and T2DM. Additionally this study showed that twice daily exenatide treatment reduces CIMT in obese T2DM patients.