The kidney plays a key role in the maintenance of the magnesium (Mg²⁺) homeostasis. Specifically, the distal convoluted tubule (DCT) is instrumental in fine-tuning of the renal Mg²⁺ handling. In recent years hereditary Mg²⁺ transport disorders have helped to identify important players in DCT Mg²⁺ homeostasis. Nevertheless, several proteins involved in DCT-mediated Mg²⁺ reabsorption remains to be discovered and a full expression profile of this complex nephron segment may facilitate the discovery of new Mg²⁺-related genes. Here, we report the Mg²⁺-sensitive expression of the DCT transcriptome. To this end, transgenic mice expressing eGFP under a DCT-specific parvalbumin promoter were subjected to Mg²⁺-deficient or Mg²⁺-enriched diets. Subsequently, the Complex Object Parametric Analyzer and Sorter (COPAS) allowed for the first time isolation of eGFP-positive DCT cells. RNA extracts thereof were analyzed by DNA microarrays comparing high vs. low Mg²⁺ to identify Mg²⁺ regulatory genes. Based on statistical significance and a fold-change of at least two, 46 genes showed differential expression. Several known magnesiotropic genes, such as Trpm6 and Parvalbumin, were upregulated under low dietary Mg²⁺. Moreover, new genes were identified that are potentially involved in renal Mg²⁺ handling. To confirm that the selected candidate genes were regulated by dietary Mg²⁺ availability, the expression levels of Slc41a3, Pcbd1, Tbc1d4 and Umod were determined by RT-PCR analysis. Indeed, all four genes show significant upregulation in the DCT of mice fed the Mg²⁺-deficient diet. By elucidating the Mg²⁺-sensitive DCT transcriptome new candidate genes in renal Mg²⁺ handling have been identified.