The karyotype of the domestic dog (Canis familiaris) is widely accepted as one of the most difficult mammalian karyotypes to work with. The dog has a total of 78 chromosomes; all 76 autosomes are acrocentric in morphology and show only a gradual decrease in length. Standardization of the canine karyotype has been performed in two stages. The first stage dealt only with chromosomes 1-21 which can be readily identified by conventional G-banding techniques. The remaining 17 autosomal pairs have proven to be very difficult to reliably identify by banding alone. To facilitate the identification of all canine chromosomes, chromosome-specific paint probes have been produced by DOP-PCR from flow-sorted dog chromosomes. Each paint probe has been used for FISH to identify the corresponding chromosome(s), allowing precise identification of all 78 canine chromosomes. The identification of the undesignated 17 autosomal pairs has been agreed upon by the standardization committee during the second stage of their role. Cosmid clones containing microsatellite markers may now be conclusively assigned to their chromosomal origin by simultaneous dual-color FISH with the corresponding paint probe. In this way a collection of chromosome-specific cosmid clones is being constructed, comprising at least one marker per chromosome, which will allow anchoring of existing and future linkage groups to the physical map.