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One of the most common scientific methods to study the chemical composition of bone matter is energy-dispersive X-ray spectroscopy (EDS). However, interpretation of the data obtained can be quite complicated and require a thorough understanding of bone structure. This is especially important when evaluating subtle changes of chemical composition, including the age-related ones. The aim of current study is to create a method of processing the obtained data that can be utilized in clinical medicine and use it to evaluate the age evolution of bone chemical composition. To achieve this goal, an elemental composition of 62 samples of cadaver compact bone, taken from the skull base (age: Me = 57.5; 21/91(min/max); Q1 = 39.5, Q3 = 73.75), was studied with EDS. We used the original method to estimate the amount of Mg 2+ cations. We detected and confirmed an increase of Mg 2+ cation formula amount in the bone apatite, which characterizes age-related resorption rate. Analysis of cation estimated ratio in a normative bone hydroxylapatite showed an increase of Mg 2+ amount (R = 0.43, p = 0.0005). Also, Ca weight fraction was shown to decrease with age (R = - 0.43, p = 0.0005), which in turn confirmed the age-dependent bone decalcification. In addition, electron probe microanalysis (EPMA) and X-ray diffraction analysis (XRD) were performed. EDS data confirmed the EPMA results (R = 0.76, p = 0.001). In conclusion, the proposed method can be used in forensic medicine and provide additional data to the known trends of decalcification and change of density and crystallinity of mineral bone matter., (© 2022. The Author(s), under exclusive licence to Springer Nature B.V.)