Obesity causes increased morbidity and mortality from metabolic and cardiovascular disease (CVD). We investigated the effect of bariatric surgery on endothelial dysfunction (ED) in retinal vessels as a marker of metabolic and cardiovascular risk in patients with obesity WHO III. Thirty consecutive patients (19/11, w/m) were evaluated by anthropometry, lipid profile, and oral glucose tolerance test before and after bariatric surgery (Mannheim Obesity Study (MOS); NCT 00770276). Risk stratification was performed by the presence of metabolic syndrome (MetS) according to ATP-III (adult treatment panel-III). Subclinical atherosclerosis was assessed by measurement of intima-media thickness (IMT). Flicker light response of retinal vessels was used as measures of ED. We measured their arteriole-to-venule ratio (AVR) for evaluation of vascular pathology. After a median of 9 months following bariatric surgery, mean weight loss was 39.4 kg (37.3%). Remission of impaired glucose metabolism was achieved in 53.3% of affected patients. Dyslipidemia improved significantly (triglycerides −61.3 mg/dl, P < 0.0001, total cholesterol −28.2 mg/dl, P = 0.002, and low-density lipoprotein cholesterol were reduced −24.5 mg/dl, P = 0.008). This resulted in a significant reduction of patients classified for MetS (27 vs. 9, P < 0.0001). Adiponectin increased by 2.08 µg/l (P = 0.032) and high sensitivity C-reactive protein (hs-CRP) and soluble intercellular cell adhesion molecule (sICAM) decreased (−7.3 mg/l, P < 0.0001 and −146.4 ng/ml, P = 0.0006). AVR improved significantly (+0.04, P < 0.0001), but neither Flicker light response nor IMT changed significantly. Retinal AVR is ameliorated after bariatric intervention. As an increased AVR results from either or both widening retinal arteriolar caliber and narrowing retinal venular caliber, an improvement in small vessel profile is evident 9 months after bariatric surgery.