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The role of magnesium in cell metabolism is complex and still not completely clarified. Although magnesium has been shown to modulate many phenomena in cells, its intracellular distribution and subcellular compartmentalization have not yet elucidated in detail, mainly as a consequence of the inadequacy of analytical techniques. The method usually employed to quantify total magnesium in cells or tissue are F-AAS or more sensitive techniques as graphite furnace AAS and inductively coupled plasma mass spectroscopy (MS). Thanks to the development of new specific fluorescent dyes, several progresses have been made in the comprehension of the fundamental biological process at the cellular and sub-cellular level. Moreover, the biological function of a chemical element in cells does not only require the determination of its intracellular quantity but also the spatial distribution of its concentration. Most of Mg2+-sensitive fluorescent dyes detect only the free metal ions, precluding the possibility of identifying the total pool of Mg. This review aims at giving an overview on different techniques focusing on two approaches to quantify total Mg in a small cell population or in single cells: i) Indirect Mg detection, label-based methods that represent the best choice to quantify the elemental concentration on a large cell population; ii) direct Mg detection (label-free), Synchrotron-based x-ray microscopy techniques that offer the possibility of achieving a detailed map of the intracellular concentration of a specific chemical element on single cell.