Bone turnover markers of resorption and formation are released during the process of bone remodelling. These markers have been extensively studied in a number of therapeutic trials of osteoporosis during the past decade. This has led to better understanding of their physiology, clinical applications and possible ways to optimize analytical techniques. Bone markers can complement the results of bone mineral density in the management of osteoporosis, but their use in clinical practice is challenged by pre-analytical and analytical variability. This review will discuss different types of bone markers, their limitations, use in different metabolic bone diseases and current recommendations from the International Osteoporosis Foundation and the International Federation of Clinical Chemistry and Laboratory Medicine bone marker standards working group.