We describe an integrated physical, genetic and cytogenetic map of human chromosome 16 comprising both a low-resolution megaYAC map and a high-resolution cosmid contig/miniYAC map, which provides nearly complete coverage of the euchromatic arms of the chromosome. The physical map is anchored to a high-resolution cytogenetic breakpoint map and is integrated with genetic and gene transcript maps of the chromosome by sequence-tagged sites and clone hybridizations.