Methylation of cytosines in DNA is an important epigenetic mechanism involved in transcriptional regulation and preservation of genome integrity in a wide range of eukaryotes. Immunoprecipitation of methylated DNA followed by hybridization to genomic tiling arrays (MeDIP-chip) is a cost-effective and sensitive method for methylome analyses. However, existing bioinformatics methods only enable a binary classification into unmethylated and methylated genomic regions, which limit biological interpretations. Indeed, DNA methylation levels can vary substantially within a given DNA fragment depending on the number and degree of methylated cytosines. Therefore, a method for the identification of more than two methylation states is highly desirable.