Chromosome analysis has been a cornerstone both for the identification of genetic defects that predispose to a variety of genetic syndromes as well as for the analysis of cancer progression. The relatively low resolution of metaphase chromosomes, however, only allows characterization of major genetic events which are defined at the megabase level. The development of the human genome-wide bacterial artificial chromosome (BACs) libraries which were used as templates for the human genome project made it possible to design microarrays containing these BACs which can theoretically span the genome uninterrupted. Comparative genomic hybridization to these arrays using test and reference DNA samples reveals numerical chromosome abnormalities (deletions, gains and amplifications) which can be accurately defined with a resolution depending on the density of the arrays. Analysis of test DNA samples using these arrays reveals low level deletions and amplifications that cannot be detected by chromosome analysis and provides a global view of these genetic changes in a single overnight hybridization using a high throughput approach. The extent of the genetic changes can then be determined precisely and the gene content of the affected regions established. These BAC arrays have widespread application to the analysis of constitutional genetic abnormalities associated with human diseases as well as cancer patients and their tumors. The development of similar BAC arrays for the mouse genome means that it is now possible to extend the CGHa approach to the study of genetic disorders and cancer models in mice.