Biochemical markers which specifically reflect either bone formation or bone resorption are helpful tools in the diagnostic and therapeutic assessment of metabolic bone disease. Bone turnover markers can be used to estimate fracture risk in postmenopausal women and older men, independent from BMD. The major domain for the use of bone turnover markers in clinical practice is the monitoring of anti-osteoporotic therapy, treatment efficacy and patient compliance. In contrast, however, bone markers cannot be used for diagnosis of osteoporosis. Measurements of markers of turnover are subject to considerable pre-analytical and analytical variability, and this problem presents a major issue in the management of osteoporosis in the clinical setting. Hence, standardisations of serum and urine collection, as well as measurement of bone markers in specialised laboratories that participate in an external quality assurance programme are mandatory.