Background: Over the past decade, the management of chronic kidney disease-mineral and bone disorder has changed substantially, altering the pattern of bone disease in chronic kidney disease. We aimed to evaluate the natural history of kidney bone disease in contemporary kidney transplant recipients and dialysis patients. Design, settings, participants, and measurement: Sixty-one dialysis patients referred to kidney transplantation participated in this prospective cohort study during November 2009 and December 2010. We performed baseline bone biopsies while the patients were on dialysis and repeated the procedure in 56 patients two years after kidney transplantation or two years after baseline if transplantation was not performed. Measurements of mineral metabolism and bone turnover as well as dual energy X-ray absorptiometry scans were obtained concurrently. Results: 37 of 56 participants received a kidney transplant, of which 27 underwent successful repeat bone biopsy. The proportion of patients with high bone turnover declined from 63% at baseline to 19% two years after kidney transplantation, while the proportion of those with low bone turnover increased from 26% to 52%. Of 19 participants remaining on dialysis after two years, 13 underwent successful repeat biopsy. The proportion of patients remaining on dialysis with high bone turnover decreased from 69% to 31%, and low bone turnover increased from 8% to 38%. Abnormal bone mineralization increased in transplant recipients from 33% to 44%, but decreased in patients remaining on dialysis from 46% to 15%. Trabecular bone volume showed little change after transplantation, but low bone volume increased in patients remaining on dialysis. Bone mineral density did not correlate with histomorphometric findings. Conclusions: Bone turnover decreased over time both in patients remaining on dialysis and in kidney transplant recipients. Bone mineral density and bone biomarkers were not associated with bone metabolism changes detected in bone biopsy.