Histones, the proteins that package eukaryotic genomes into chromatin, are subject to a huge number and variety of covalent modifications. In the past few years, genomic technologies such as microarray hybridization have been applied to the study of histone modifications. These studies shed significant light on the role of covalent modifications in DNA-templated processes. Different histone modifications exhibit distinctive patterns over underlying genomic elements, and these localization patterns reflect the regulatory functions of the relevant modifications. For example, recent results indicate that the localization of H3K36me3 over coding regions reflects its role in shutting down internal transcriptional initiation sites. Histone modifications occur in domains of varying sizes, and the locations of the broadest domains of modifications suggest that broader domains are more likely to be heritable than are shorter modification domains. Importantly, genomic studies reveal that histone modifications tend to co-occur in groups, suggesting that the purpose of histone modifications is not to generate an intricate, complex code, and once again raising the question of why so many histone modifications exist in the cell.