This chapter summarizes information concerning genetic as well as local and systemic factors involved in the etiology and pathogenesis of rare bone diseases where data from assays of biochemical markers of skeletal remodeling are accumulating. For such disorders, bone turnover assessed biochemically can shed light on the nature of the skeletal perturbation and help to design, evaluate, and monitor treatment. However, systemic or focal derangements in bone growth, modeling, and remodeling and cartilage formation and degradation can be occurring and lead to generalized or regional ostopenia (bone density below the normal) or increases in skeletal mass. Biochemical markers of skeletal formation or resorption provide summative values reflecting the impact of a global disturbance or a partly localized lesion. Hence, the type and extent of the pathologic process in individual patients merits consideration when interpreting results from such assays. This is best illustrated by the common focal skeletal disorder, Paget's bone disease.