Postprandial hyperinsulinemia characterizes Roux-en-Y gastric bypass (RYGB) and sometimes leads to reactive hypoglycemia. We prospectively evaluated changes in beta cell function in seven RYGB-operated patients with a median follow-up of 2.9 years with hyperglycemic clamps and oral glucose tolerance tests (OGTTs). Three years after RYGB, weight loss was 26 % and insulin sensitivity had improved. Insulin secretion during clamp experiments was largely unchanged compared to before surgery. In contrast, insulin secretion in response to the OGTTs doubled when evaluated by the disposition index and 2-h plasma glucose declined to a mean of 3.3 ± 0.3 mmol/l postoperatively. Our findings indicate that intrinsic beta cell function remains unchanged in glucose-tolerant patients even years after RYGB, while altered gut-islet regulation drive risk of postprandial hyperinsulinemic hypoglycemia.