Aim To investigate whether Roux-en-Y gastric bypass surgery (RYGB) - an in vivo model for normalisation of hyperglycaemia - improves carotid intima-media thickness (IMT) in patients with type 2 diabetes (T2D)/impaired glucose tolerance (IGT) and normal glucose tolerance (NGT). Methods Observational prospective study, 34 obese patients (T2D (n = 14)/IGT (n = 4), and NGT (n = 16)) were investigated before and six and 12 months after RYGB. Results Mean carotid IMT was significantly reduced 12 months after RYGB in patients with T2D/IGT (- 0.041 mm (95% CI - 0.069; - 0.012, p = 0.005)) but not in patients with NGT (- 0.010 mm (- 0.039; 0.020, p = 0.52)). The between-group difference was not significant (p = 0.13). Twelve months after RYGB, patients with respectively T2D/IGT and NGT demonstrated changes in weight: - 29.9 kg, p < 0.001/- 30.6 kg, p < 0.001, HbA1c: - 0.7%, p < 0.001/- 0.1%, p = 0.33, systolic blood pressure: - 2 mmHg, p = 0.68/- 10 mmHg, p = 0.01 and diastolic blood pressure: - 8 mmHg, p = 0.003/- 11 mmHg, p < 0.001. 80% of T2D patients terminated antihyperglycaemic medication. Conclusion Mean carotid IMT was significantly reduced 12 months after RYGB in patients with T2D/IGT which provides evidence to support that the earliest atherosclerotic changes in the arterial wall are reversible. Although numerically different from the changes observed in patients with NGT, the between-group difference was not statistically significant.