Magnesium deficiency is associated with a set of abnormalities in pregnant women, with fetal malformation, complicated neonatality and early childhood, as well as comorbidities (atherosclerosis, hypertension, obesity, coronary heart disease, cerebrovascular disease, osteoporosis, etc.) at mature and elderly ages. Magnesium deficiency (ICD-10 E61.2) is clinically diagnosed; the quantification of magnesium in different biological substrates may give a comprehensive idea of its status. Analysis of the levels of magnesium in a few biological substrates (whole blood, red blood cells, plasma, serum, saliva, urine, nails, and hair) simultaneously taken from the same patient can identify their impaired magnesium distribution typical for this or that disease. This paper gives the results of systematization of the available data on the reference values of magnesium in different biological substrates (plasma, serum, whole blood, red blood cells, saliva, urine, and hair). It sequentially considers methods for the laboratory diagnosis of magnesium deficiency and the specific features of determination of the concentrations of this compound in blood, daily urine, saliva, and hair. The results of clinical, epidemiological, laboratory, and clinical studies and evidence-based medicine are presented.