Introduction: Disorders of minerals metabolism are common metabolic problems in patients undergoing peritoneal dialysis (PD) which causes increase in mortality and morbidity in these patients. Objectives: In this study, the relationship between bone metabolic indices and mortality rate in patients on PD was assessed. Patients and Methods: Data were collected from Iranian peritoneal dialysis registry database, covering the period 2009–2015 and comprised 2000 adult patients. Patients with less than three months follow-up and incomplete data were excluded. Demographic and some laboratory data (including age, gender, body mass index, serum albumin, dialysis vintage and comorbidities) of patients recorded. Additionally, the unadjusted and adjusted, hazard ratios (HRs) of serum phosphorus (P), calcium (Ca) and parathyroid hormone (PTH) levels, to find their association with mortality were calculated, using the Cox proportional-hazards model. Results: In total, 1197 out of 2000 patients had the inclusion criteria and were included in the study. We found that serum iPTH (intact parathyroid hormone) over 600 pg/mL significantly increased the mortality rate by 2.7 times compared to iPTH levels between 200 to 600 pg/ mL (HR: 2.7, P=0.002). Additionally, the serum phosphorus level less than 4 mg/dL was significantly (P=0.0001) related to higher mortality rate (HR: 1.6). There was no significant association of serum calcium and alkaline phosphatase (ALP) levels with mortality (P > 0.05). Conclusion: Although high serum iPTH and low-serum phosphorus levels could determine the mortality risk in PD patients, Ca and ALP levels were not risk factors for mortality.