Bone histomorphometry has been the gold standard in the evaluation and diagnosis of renal osteodystrophy. The recent new definition of renal osteodystrophy as chronic kidney disease-mineral and bone disorder has once again highlighted the use of bone biopsy as a powerful and diagnostic tool to determine skeletal abnormalities in chronic kidney disease. The procedure of iliac crest bone biopsy has been proved safe and associated with very minimal morbidity. In this review, the clinical indications, preparation, instrumentation, and potential complications are discussed. Because current biochemical markers are poor predictors of bone turnover, volume, and mineralization, a wider use of bone biopsy and histomorphometry will lead to a better understanding of the bone and mineral disorders that are associated with chronic kidney disease.