Bone turnover markers assist in fracture risk prediction, management and monitoring of osteoporosis in patients without chronic kidney disease (CKD). The use in CKD-mineral bone disorder (MBD) has been limited as many of these markers and breakdown products are renally excreted, including the most commonly used and well standardized procollagen type I N propeptide and C-terminal cross-linking telopeptide of type I collagen. Of the markers unaffected by renal function, bone specific alkaline phosphatase is associated with mortality and fracture rate in CKD subjects and is now available on several automated analysers. When used in combination with PTH, bone specific alkaline phosphatase as a bone formation marker correlated well with bone biopsy histomorphometry in predicting adynamic bone disease. Tartrate-resistant acid phosphatase 5b is a resorption marker that is under development for automation. Both high and low bone turnover in CKD-MBD patients are associated with increased fracture and mortality risk. Bone biopsy as the gold standard to differentiate between adynamic bone disease and osteitis fibrosa is limited by availability and cost. Appropriate use of bone turnover markers is vital in the decision to commence anti-resorptive agents, and to monitor efficacy in order to avoid over suppression of bone turnover, which may lead to stress fractures. Further efforts are required to develop markers unaffected by renal function with standardized cut-off values and fracture as well as vascular calcification end-points.