DNA methylation is an important regulatory step in gene expression. Knowledge of the alterations in DNA methylation at a whole genome scale improves our understanding of gene regulation and potential correlations with biological events or disease progression. Methylated DNA immunoprecipitation (MeDIP) uses an antibody that efficiently enriches methylated DNA fragments for downstream locus-specific or genome-wide analyses. MeDIP-on-Chip uses the MeDIP approach in combination with a tiling array for the investigation of genome-wide DNA methylation patterns (or DNA methylomics). The following protocol describes the application of MeDIP to the hybridization of DNA microarrays and data analysis.