Background/Aims: The Mineral and Bone Disorder Outcomes Study for Japanese CKD Stage 5D Patients (MBD-5D) is a multicenter, prospective observational study of hemodialysis patients with secondary hyperparathyroidism (SHPT) in Japan, where the national guideline recommends targets for serum calcium (8.4–10.0 mg/dl), phosphorus (3.5–6.0 mg/dl), and intact parathyroid hormone (PTH) (60–180 pg/ml). Methods: The MBD-5D involved patients who were receiving hemodialysis for more than 3 months and met at least one of the following conditions: having intact PTH levels >180 pg/ml, or receiving intravenous vitamin D receptor activators (VDRAs) or oral VDRA analog. This report describes the baseline characteristics of the study participants and examines factors associated with mineral metabolism controllability. Results: A total of 8,229 patients were registered from 86 facilities as the whole cohort, and 3,276 patients were randomly selected as the subcohort. The severity of SHPT was associated with a lower likelihood of achieving the targets for calcium and phosphorus, whereas patients with a history of parathyroidectomy were more likely to achieve these targets as compared with those who had not undergone surgery despite high PTH levels. The use of 2.5 mEq/l calcium dialysate was also associated with a higher likelihood of achieving the targets compared with the use of 3.0 mEq/l calcium dialysate. Conclusion: The severity of SHPT and the use of dialysate with higher calcium concentration are associated with practical difficulty in managing mineral metabolism in dialysis patients. Further prospective follow-up is needed to confirm our findings and to examine their impact on patient-level outcomes.