This study evaluated early and medium-term changes in bone turnover markers, and their associations with weight loss, total bone mineral density (BMD), and hormonal changes after biliopancreatic diversion (BPD). Ancillary study from a one-year prospective cohort of 16 individuals assessed before, 3days, 3 and 12months after BPD. Bone turnover markers (C-terminal telopeptide (CTX), intact osteocalcin (OC), sclerostin, and osteoprotegerin (OPG)) and several hormones were measured at each visit. Total BMD by DXA was assessed at baseline, 3 and 12months after BPD. Three participants were lost to follow-up. CTX increased significantly at 3days (+ 66%), 3months (+ 219%), and 12months (+ 295%). OC decreased at 3days (- 19%) then increased at 3months (+ 69%) and 12months (+ 164%). Change in sclerostin was only significant between 3days and 3months (+ 13%), while change in OPG was significant between baseline and 3days (+ 48%) and baseline and 12months (+ 45%). CTX increase correlated negatively with weight loss at 3 (r = - 0.63, p = 0.009) and 12months (r = - 0.58, p = 0.039), and total BMD decrease (r = - 0.67, p = 0.033) at 12months. Change in insulin and adiponectin correlated with changes in bone turnover markers independently of weight loss. BPD causes an earlier and greater increase in bone resorption over bone formation markers and a decrease in total BMD. Sclerostin did not increase as expected following extensive weight loss. Changes in insulin and adiponectin seem to play a role in the activation of bone remodeling after BPD.