By two-dimensional (2-D) DNA typing several hundred genomic loci can be analysed simultaneously in a two-dimensional pattern as spots detected by micro- or minisatellite core probes. Many of these loci display DNA sequence polymorphisms, and we have examined whether it is possible to extract genetic information from the rather complex but potentially very informative 2-D DNA typing patterns. To do so, the segregation of 9 spots detected by the microsatellite core probe (CAC) n was followed in a large CEPH pedigree, and by linkage analysis it was possible to obtain chromosomal assignments of the corresponding (CAC)n loci in all cases except one. Furthermore, a regional, physical localization of these loci emerged from analysis of the existing genetic and physical localization data of DNA markers flanking the (CAC)n loci. We have hereby obtained evidence that the spots detected by the microsatellite core probe (CAC)n segregate in a Mendelian manner and that it is possible to reliably score the segregation of single spots within a family. These results indicate that the large amount of potential information inherent in 2-D DNA typing may be used as a genetic marker system; an important prerequisite for its application as a genome scanning method, e.g. in detection of genomic alterations in cancer and in mapping of genetic traits.