The analysis of epigenetic changes in genomic DNA has seen an exponentially increasing interest over the last years. Within the field of epigenetics DNA methylation patterns have become of particular interest to the scientific community. The covalent addition of a methyl group to cytosine bases in the CpG dinucleotide sequence holds particular analytical advantages. Working with DNA as an analyte molecule is robust and samples are unproblematic to collect and handle. Also changes in DNA methylation are a dynamic process and the resulting patterns are tightly associated to disease. This combination of robust technical performance and disease-specific methylation patterns might enable DNA methylation as a powerful biomarker in the future. The increased interest has triggered exciting new findings which ultimately show that epigenetic regulation of gene expression is not a binary system. On the contrary, especially the quantitative measure DNA methylation has greatly contributed to the areas of gene regulation, developmental biology, and translational medicine. Performing quantitative methylation measurements in large scale used to be impaired by the limitations of measurement technologies. They either suffered from limited throughput, limited accuracy, high cost, or a combination of those. Here we introduce a new technique that combines candidate gene amplification with base-specific cleavage or primer extension methods and MALDI-TOF mass spectrometric analysis to overcome the described limitations.