There is much interest in the gene content of the small heterochromatic W chromosome of the chicken, on the supposition that it may contain sex-determining genes. A considerable region in the chicken genome has been assigned to the W chromosome on the basis of its repetitive sequences. Using fluorescent in situ hybridization (FISH) we localized five Bacterial Artificial Chromosomes (BACs) onto female chicken metaphase spreads. We physically mapped these BACs to the Z chromosome. The chicken genome database, however, assigned all five BACs to the W chromosome. Our results demonstrate that the 17 genes on these BACs are Z-specific, and points to the inadequacy of assigning regions of the genome based exclusively on repetitive sequences.