The pattern of ion substitutions and non-stoichiometry of oxalate and phosphate human body minerals (weddellite, whewellite, hydroxyapatite, struvite, and brushite) and their synthetic analogs was investigated by complex X-ray diffraction, spectroscopic, and chemical methods. All the studied biological minerals are characterized by variable non-stoichiometry composition that reflects the non- stationarity of formation conditions. Non-stoichiometry of calcium oxalates results from variations in quantities of disorderly distributed water molecules. The water amount in weddellite significantly influences the crystal structure parameters. In particular, there is positive correlation between the value of a parameter and the occupancy of “zeolitic” water sites. Variations in composition of calcium and magnesium phosphates are caused by substitutions at all the crystallographic sites. Ion replacements in apatite and struvite are more prominent in comparison with those in brushite. Non-stoichiometry of apatite and brushite is due to the presence of vacancies at the Ca-sites, and that of struvite is due to the vacancies at the Mg-site. Two types of non-stoichiometry in carbonated apatites of B-type realize due to replacements PO43− ← CO32− or OH− ← H2O. Maximum concentrations of impurity ions in magnesium and calcium phosphates are mainly limited by the content of these ions in the physiological solution. In case of Mg replacement with Ca in struvite and Ca with K in brushite and apatite, it is also essentially limited by the size differences of the host and admixture ions.