The combination of genomic microarrays with comparative genomic hybridization and with chromatin immunoprecipitation is providing an increasingly detailed view of the way in which the human genome is organized and functions and how disorganization and disfunction can lead to disease. These studies are enhanced by the flexibility of array technology, allowing resolutions from coverage of the whole genome using 200 kb cloned DNA inserts to detailed analysis using PCR products or oligonucleotides of 100 bp or less. In particular, the use of chromatin immunoprecipitation is providing new insights into chromosome structure and gene regulation and control through the analysis of protein--DNA interactions.