BACKGROUND Biliopancreatic diversion with duodenal switch, BPD-DS, is a surgical procedure for treatment of super obese patients. It renders very good weight results and it strongly reduces the incidence of type 2 diabetes. One important mechanism of weight reduction after BPD-DS is malabsorption. Hypomagnesemia is an established cardiovascular risk factor. While it is well-known that magnesium levels decline after jejuno-ileal bypass and increase after gastric bypass surgery, information on how magnesium status is affected by BPD-DS is scant. The aim of the present study was to evaluate plasma magnesium concentrations (P-Mg) after BPD-DS. METHODS Thirty-one patients, all Caucasians (9 diabetics, 12 men, age 38 ± 8 years, weight 159 ± 22 kg, body mass index (BMI) 53.9 ± 5.2 kg/m(2)) underwent BPD-DS. We evaluated weight, glycated hemoglobin levels (HbA1c) and P-Mg preoperatively as well as at 1 and 3 years after surgery. All subjects were treated with vitamin and mineral substitution after surgery, including 100 mg of magnesium salt. P-Mg was analyzed with respect to changes over time, correlation to BMI and HbA1c levels before and 3 years after surgery. RESULTS The plasma magnesium concentrations increased by 15 % from 0.77 ± 0.07 to 0.88 ± 0.09 mmol/l over 3 years (p < 0.001). The weight loss was 71 ± 25 kg. No patient had diabetes at follow-up. No correlations between P-Mg and BMI or HbA1c were seen. CONCLUSIONS Although exerting much of its weight-reducing effect by a malabsorptive mechanism, BPD-DS yields a rise in P-Mg 3 years postoperatively, possibly contributing to the improved metabolic state after this operation.