Methylation of cytosines is the key epigenetic modification of DNA in eukaryotes and is associated with a repressed chromatin state and inhibition of gene expression. The methylation pattern in mammalian genomes is bimodal, with most of the genomes methylated except for short DNA stretches called CpG islands (CGIs), which are generally protected from methylation. Recent technical advances have made it possible to map DNA methylation patterns on a large scale. Several genomic studies have made significant progress in unraveling the intricate relationships between DNA methylation, chromatin structure, and gene expression. What is emerging is a more dynamic and complex association between DNA methylation and expression than previously known. Here we highlight several recent genomic studies with an emphasis on what new information is gained from these studies and what conclusions can be reached about the role of DNA methylation in controlling gene expression.