The magnesium concentrations in plasma and cells could be affected by diet, disease and genetic factors. To characterise the genetic factors involved in the regulation of magnesium homeostasis, Low (MgL) and High (MgH) magnesium status mice were developed by bidirectional selective breeding. The effects of a low-magnesium diet on the magnesium status parameters were analysed in these mice. Using a cDNA array, a screen for differential gene expression was performed in kidneys from these animals, fed either a magnesium adequate or deficient diet. The magnesium-deficient diet significantly affected the plasma, erythrocyte and urine magnesium concentrations in both strains, in similar proportions in the two strains. Furthermore, in response to the magnesium-deficient diet, both strains showed changes of the expression of genes belonging, for the majority of them, to the family of transcription and growth factors (down-regulated). Of the identified genes, five were of particular interest because they were differently expressed in response to the deficient diet in these two strains: osteopontin, the cholecystokinin A receptor, connexin 45, a growth hormone receptor and BAG1. These results suggest that the two strains exhibit different physiopathological responses to magnesium deficiency.