The Cancer Chromosome Aberration Project generates a repository of BAC clones with a resolution of 1–2 megabases. The cytogenetic location of all clones is established by high-resolution fluoresence in situ hybridization mapping onto prometaphase chromosomes. Linkage to existing physical maps is provided by the requisite presence of a mapped sequence tagged site in all selected BACs and in many cases by the full or end sequencing of the mapped clone itself. Clones in the repository should allow all chromosomal breakpoints to be localized to within 2 Mb and provide entry points to existing physical maps of the intervening distance. With the completion of a rough draft of the human genome, sequences between mapped breakpoints can be immediately queried for potential candidate genes. We will provide an update on the number of BAC clones and chromosomes currently mapped and available to the biomedical community. One critical issue is the integration of databases for the cytogenetic and physical maps. The National Cancer Institute and National Center for Biotechnology Information are working together to develop a meaningful integration that provides (1) a direct connection between catalogued and newly discovered chromosomal breakpoints or regions of genomic imbalances and the BAC clone set; (2) direct display of recurring chromosomal breakpoints that coincide with BAC locations; (3) placement of mapped BACs on the human sequence; (4) tools to build contiguous clone sets; (5) integration of the BAC clone set with databases for comparative genomic hybridization and spectral karyotyping and (6) an interface for the identification of orthologous regions of chromosomal aberrations in human cancers and their respective mouse models.