DNA microarrays are increasingly being used to investigate the functional role of chromatin. These studies are enhanced by the development of high-resolution arrays covering either the whole genome or specific regions of selected chromosomes with large insert clones, PCR products or oligonucleotides of around 100 bp or less. In combination with chromatin immunoprecipitation, this approach allows identification of protein binding for transcription factors, proteins involved in DNA replication and repair as well as sites of chromatin modification. Furthermore, by application of S phase fractions to genomic microarrays, replication timing can be estimated. Thus, microarrays can provide new information about chromosome structure and gene regulation.