DNA methylation-dependent gene silencing is one of the most characterized mechanisms in epigenetic regulation of gene expression. This process is thought to influence the ability of hepatocyte nuclear factor 1 (HNF1) to transactivate organic anion transporter expression in the liver and kidney. To evaluate this further we profiled 282 mouse solute carrier transporters by examining regions near their transcription start sites for tissue-dependent differentially methylated regions (T-DMR) using restriction tag-mediated amplification to determine T-DMR disparity between the liver and kidney. Forty-two of these were associated with T-DMR tags hypomethylated in the kidney but hypermethylated in the liver. Computational analysis found a canonical HNF1-binding motif within 1 kbp of the promoter region of 13 carriers including the amino acid transporters Slc6a19, Slc6a20, Slc7a8 and Slc7a9; all expressed predominantly in the kidney. Bisulfite genomic sequencing found that CpG dinucleotides neighboring the T-DMR tags were hypomethylated in the kidney compared with the liver. The Hnf1 alpha promoter region itself contained a T-DMR hypomethylated in the liver and kidney but hypermethylated in the cerebrum, consistent with the tissue distribution of Hnf1 alpha. Taken together, our results show a central role of DNA methylation in the kidney-specific expression of amino acid transporters thus determining both the tissue distribution of their master regulator, Hnf1 alpha, and its interaction with downstream genes. Kidney International (2010) 78, 569-577; doi:10.1038/ki.2010.176; published online 16 June 2010