Background: CKD-MBD is abnormalities in mineral metabolism and bone structure in patients with chronic kidney disease (CKD). Many children with glomerulonephritis progress to CKD. In many patients with primary or secondary glomerulonephritis, the use of immunosuppressant may cause osteoporosis and growth retardation. We evaluated the effect of immunosuppressant on CKD-MBD in children. Methods: KNOW-pedCKD is a Korean cohort study for outcomes in patients with pediatric CKD for 10 years which started from April 2011. 437 patients with CKD stage I to V predialysis below 18 years of age were included. We divided the patients into 3 groups according to CKD stages: CKD stage I-II (188 patients), stage III (139 patients) and stage IV-V (109 patients). We compared serum corrected total calcium, phosphorus, alkaline phosphatase (ALP), intact parathyroid hormone ( PTH), vitamin D, and trans-tubular reabsorption of phosphorus (TRP) between patients who had immunosuppressants (IS group) and those without drug treatment (non-IS group) in each CKD group. Results: In IS group, serum calcium (9.16±0.58 vs 9.37±0.54 mg/dL, p=0.050), serum calcium x phosphorus (39.81±9.84 vs 44.32±9.09, p=0.029), and intact PTH (55.96±29.16 vs 83.70±67.20 pg/mL, p=0.037) level was lower in CKD stage III, serum alkaline phosphatase was lower in CKD stage III (161.3±132.3 vs 259.1±1176.3 IU, p0.001) and IV-V (117.8±146.5 vs 278.6±165.7 IU, p=0.002), calcidiol level was lower in CKD stage I-II (17.11±8.93 ng/mL vs 23.07±10.96, p=0.002), and TRP was higher in CKD stage IV-V (73.78±8.79% vs 54.37±21.09, p0.001). Conclusion: The use of immunosuppressant in pediatric CKD patients may worsen CKD-MBD which was associated with hypocalcemia, low alkaline phosphatase, and low PTH.