Purpose: Bariatric surgery (BS) is becoming an increasingly frequent treatment option especially in people with morbid obesity, demonstrating that it is able to reduce total mortality and cardiovascular (CV) risk. Despite endothelial dysfunction is an essential requisite contributing to atherosclerosis and predicting CV events, only some studies have investigated the effects of BS on endothelial function with controversial results. In this study, the effects of weight loss on endothelial function were investigated in obese patients after BS and compared with patients after medical nutrition treatment (MNT). Patients and Methods: Seventeen obese patients who underwent BS procedures (9 adjustable gastric bands, 3 gastric by-passes and 5 biliopancreatic diversions) were included in the study and compared with 18 obese individuals who underwent MNT. Endothelial function was investigated by flow-mediated dilation (FMD) of the brachial artery. Also, carotid intima-media thickness (c-IMT) was measured as a marker of subclinical atherosclerosis. Results: At the end of follow-up, the mean weight loss was 18.8% in the BS group and 7.0% in the MNT group. After treatment, FMD significantly decreased in the BS group (mean ± SD before: 9.0 ± 4.7; after: 6.1 ± 2.9%; P= 0.04); however, no significant change was observed in the MNT group (before: 9.4 ± 5.8; after: 8.3 ± 5.3; P= 0.41). The modification of endothelial function was negatively correlated with c-IMT change in the BS group (r= −0.63; P <0.007). Conclusion: A significant endothelial dysfunction occurred following BS but not after MNT. Furthermore, the decline of endothelial function observed in the BS group might have contributed to atherosclerosis.