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The blood-brain barrier (BBB) tightly regulates the homeostasis of the central nervous system, and its dysfunction has been described in several neurological disorders. Since magnesium exerts a protective effect in the brain, we assessed whether supraphysiological concentrations of different magnesium salts modulate the permeability and magnesium transport in in vitro models of rat and human BBB. Among various formulations tested, magnesium pidolate was the most efficient in reducing the permeability and in enhancing magnesium transport through the barrier. We then compared magnesium pidolate and magnesium sulfate, a widely used salt in experimental models and in clinical practice. Magnesium pidolate performs better than sulfate also in preventing lipopolysaccharide-induced damage to in vitro generated BBB. We conclude that magnesium pidolate emerges as an interesting alternative to sulfate to protect BBB and maintain correct intracerebral concentrations of magnesium.