Methods for analyzing DNA methylation profiles in genomes. Step-by-step protocols are available for procedures in boldface (for gene-specific analysis, see Protocol: DNA Bisulfite Sequencing for Single-Nucleotide-Resolution DNA Methylation Detection [Lizardi et al. 2017a]; for methylation-specific PCR, see Protocol: Methylation-Specific Polymerase Chain Reaction (PCR) for Gene-Specific DNA Methylation Detection [Lizardi et al. 2017c]; for gene-specific PCR, see Protocol: Methyl-Cytosine-Based Immunoprecipitation for DNA Methylation Analysis [Lizardi et al. 2017d]; for deep sequencing after methylation-specific restriction digestion, see Protocol: High-Throughput Deep Sequencing for Mapping Mammalian DNA Methylation [Lizardi et al. 2017e]; and for deep sequencing after bisulfite conversion, see Protocol: Illumina Sequencing of Bisulfite-Converted DNA Libraries [Lizardi et al. 2017b]).