Roux-en-Y gastric bypass is associated with increased risk of bone fractures. Malabsorptive procedures may be associated with secondary hyperparathyroidism and detrimental effects on bone health. We aimed to compare the effects of standard and distal gastric bypass on bone turnover markers 2years after surgery. Patients with body mass index (BMI) 50-60kg/m2 (n = 113) were randomized to standard or distal gastric bypass, 105 patients (95%) completed 2-year follow-up. Serum C-terminal telopeptide of type I collagen (CTX-1), procollagen type I N-propeptide (PINP), and bone-derived alkaline phosphatase (BALP) was measured at baseline and up to 2years after surgery. ANCOVA and linear mixed models were used to compare groups. The levels of bone turnover markers increased significantly in both groups, with no statistically significant difference between groups. Two years after standard and distal gastric bypass mean (SD) CTX-1 were 0.81 (0.32) and 0.83 (0.31) μg/L (p = 0.38), mean PINP was 77.6 (23.2) and 77.7 (29.3) μg/L (p = 0.42), and BALP 47.9 (21.9) vs. 50.7 (19.6) μg/L (p = 0.38), respectively. Multiple linear regression analyses showed that PINP and BALP correlated positively (p = 0.01 and p < 0.001) with PTH, but only BALP was significantly higher in patients with secondary hyperparathyroidism (p = 0.001). Type of surgery, vitamin D serum concentrations, and 2-year BMI were all independently associated with PTH levels. A comparable increase in bone turnover markers 2years after standard and distal gastric bypass was observed. There was a higher prevalence of secondary hyperparathyroidism after distal gastric bypass, but this did not impact bone turnover markers. Clinical Trials.gov number NCT00821197.