Introduction: The prevalence of bone mineral disorder is best known in end-stage renal disease (ESRD) patients, but less data is available for the earlier stages. Objectives: We aimed to compare the prevalence of bone metabolic disorder at all stages of chronic kidney disease (CKD) and assess its contribution to CKD progression and patients’ outcome. Patients and Methods: In a retrospective cohort study, CKD patients who were under treatment for three years were selected from a nephrology clinic in Tehran, Iran. Patients’ demographic and laboratory data, as well as the outcome of their treatment were gathered and analyzed. Results: In 473 patients with an average age of 61.5, 60.1% were at stage III, 35.8% were at stage IV, and 4.1% were at stage V of CKD. There was a significant relationship between CKD stage and serum phosphate, calcium-phosphate product, and systolic blood pressure (SBP). Furthermore, the patients’ outcome was significantly related to advanced stages of CKD, higher first phosphate level, diabetes mellitus in medical history, and higher stages of SBP. By multiple Cox regression analysis, after adjustment for glomerular filtration rate (GFR), the first serum phosphate level, and the calcium-phosphate product did not contribute to the undesirable outcome. Conclusion: Although bone metabolic disorder is more frequently seen in advanced stages of chronic kidney disease, these changes can be seen even in earlier stages of the disease. The influence of phosphate abnormality in the patients’ outcome should be studied more in earlier stages for better control.