Completion of draft and near complete human chromosomal DNA sequences permits a genome-wide analysis of the relationship between genetic and physical map distances. Using computer searches we have identified BAC sequences which encompass about 70% of the 8000 short tandem repeat polymorphisms (STRPs) on our most recent comprehensive genetic maps (Broman et al. Am. J. Hum. Genet. 63:861-869, 1998). Reasons for the 30% failure are not completely understood, but likely involve absence of the appropriate BAC sequence from the public database and the presence of interspersed repeats within the STR sequence. At the time of abstract submission (June 2000), we have obtained reliable physical distances in nucleotides between STRPs for three chromosomes: 6, 21 and 22. Physical distances for the remaining chromosomes are likely to become available in the near future. Comparison of the genetic and physical maps helps identify errors in the maps, regions of high and low recombination, and even putative inversion polymorphisms. For chromosomes 6, 21, and 22, marker orders agreed well between the genetic and physical maps. Only four STRPs appeared to be positioned with large error. Overall recombination rates (sex-average) for the three chromosomes ranged from 1.1 to 1.9 and averaged 1.24 cM/mb. For many chromosomal regions, female and male recombination rates changed in parallel, but for other regions there were large gender differences. Regions with particularly low recombination, near 0 cM/mb and spanning 6 - 12 mb, were found on all three chromosomes. Genes within these recombination deserts may be particularly amenable to mapping by association. Regions with particularly high average recombination, up to about 6 cM/mb were also identified. It is unknown if these recombination jungles have uniformly high levels of recombination or are in turn comprised of shorter regions of high and low recombination.