Biochemical markers of bone turnover detect activity of bone cells, namely osteoblasts and osteoclasts. Osteoclasts resorb bone, and fragments of collagen type I (telopeptides, pyridinolines) are released into extracellular fluid and subsequently transported in blood and urine. Osteoblasts synthesise bone matrix proteins, among which are some of clinical significance: collagen type I propeptide, osteocalcin and bone alkaline phosphatase. Considerable scientific evidence has demonstrated that biochemical markers of bone turnover enable insight into dynamics of bone turnover, growth and repair. The most comprehensive data are available for the monitoring of osteoporosis treatment effects, for which use clinical guidelines have been defined. Measurement of biochemical markers of bone turnover in other metabolic bone disorders and malignant diseases with skeletal involvement is important in diagnostic assessment and therapy monitoring. Interpretation of results should take into consideration biological variations of these analytes.