Patients with severe obesity submitted to Roux-en-Y gastric bypass (RYGB) are at risk of developing long-term hypovitaminosis D and secondary hyperparathyroidism (SHPT) as well as osteometabolic disease. This study aimed to evaluate calcium-vitamin D-PTH axis and bone mineral density (BMD) changes from post-RYGB patients who were followed-up until a median of 5 years. Vitamin D deficiency was defined as 25-hydroxyvitamin D <20 ng/mL and SHPT as PTH >68 pg/mL, in patients with normal serum creatinine and calcium. BMD was estimated by dual-energy X-ray absorptiometry (DXA, g/cm2). We included 127 post-RYGB patients (51±10.6 years, 87.4% self-declared White, 91.3% female, 52.8% postmenopausal). Vitamin D deficiency prevalence was the highest (41.5%) in the second year and the lowest (21.2%) in the third year (p<0.05). SHPT prevalence was 65.4% in the second year and increased to 83.7% in the sixth year (p<0.05). Patients with low BMD in lumbar, femoral neck, and total proximal femur were older and presented menopausal status more frequently than normal BMD group (p<0.05). Older age was a risk marker for altered BMD in femoral neck (OR=1.185; 95% CI 1.118-1.256) and in total proximal femur (OR=1.158; 95% CI 1.066-1.258), both after adjusting for follow-up and excess weight loss. After 5 years, most bariatric patients presented calcium-vitamin D-PTH axis disruption, in which SHPT was more frequent than hypovitaminosis D. Older patients and menopausal women presented higher rates of low BMD, and older age was a risk marker, especially for low BMD in femoral sites.