Pseudoxanthoma elasticum (PXE) is a heritable connective tissue disease caused by mutations in the ABCC6 gene that encodes a transmembrane transporter of unknown function, expressed mainly in the liver. It has been suggested that some PXE patients for whom no mutations can be found in the coding region of ABCC6 probably suffer from insufficient level of active protein due to lowered gene expression. Here we report the functional analysis of previously reported natural polymorphisms found in the ABCC6 gene promoter. The only polymorphism known to be significantly more common in PXE patients was located within one of the PLAG transcription factor binding sites located by us previously. This mutation negatively influenced PLAG-mediated induction of ABCC6 promoter in a reporter gene system. Moreover, site-directed mutagenesis of an analogous sequence within another PLAG-binding site in the promoter both depressed PLAG binding and specifically repressed ABCC6 promoter activity in cells of liver origin. Thus, we have identified novel sequence determinants of liver-specific transcription of the ABCC6 gene with direct relevance for at least some PXE patients.