Children and adolescents may be affected by a host of metabolic diseases that primarily impact the integrity of the skeletal system. Often, the underlying problem involves impairment in calcium, phosphate or vitamin D homeostasis. Alternatively, hormonal imbalances, such as in parathyroid hormone, may be at the heart of the problem. Recent advances in our diagnostic capabilities, such as the wide availability of assays for parathyroid hormone, ionized calcium, and vitamin D metabolites; genetic testing for hereditary disorders of bone; and widespread use of bone densitometry technologies, have improved our diagnostic acumen. However, at the same time, familiarity with these new developments is limited and may lead to misinterpretation without a careful understanding of certain features of these tests. Thus, our mission is to discuss the strengths and shortcomings of these diagnostic modalities and to provide a concise review of nuances involved in interpretation of data when using these techniques.