The results of experiments aimed at detecting polymorphisms and mutations in the BRCA1 promoter region as well as comparisons of two published DNA sequences indicated that two similar but distinct copies of this region exist in the human genome. PCR primers specific for amplification of each of the related sequences were developed and new genomic clones corresponding to each of the two promoter regions were isolated from rearrangement-resistant libraries. Sequence analysis of the clones and specific PCR products reveals two similar genomic arrangements of head-to-head genes. The BRCA1 gene is closely apposed to a gene structure that is similar but not identical to 1A1.3B, and the 1A1.3B gene is apposed to a gene structure that has strong similarity to BRCA1 but also significant differences. STS analysis of YAC and P1 clones located in the vicinity of BRCA1 indicates that these similar promoter regions are elements of a direct duplication. New hypotheses for genetic mechanisms that may be involved in breast and ovarian cancer etiology are raised by the identification of this duplicated genetic structure on chromosome 17q.