To determine the genetic causes of phenotypes, it is necessary to characterize the actual genotypic variation within linkage distance of the causative genetic code. There is however little knowledge about the DNA-variation in the Norwegian population. Due to founder effects after narrow bottleneck-events like the last ice age and the bubonic plague followed by rapid expansion, there are reasons to believe that the Norwegian population contains genomic imbalances that makes this population valuable for association- and linkage analysis. A system of known polymorphic markers across the Norwegian genome would therefore represent an important resource for solving a large range of clinical problems. This project represents a first effort to make such a map with a resolution of about 5cM restricted to chromosome 13 utilizing an in-house platform of cycling gradient capillary electrophoresis (CGCE). We have established allele frequencies for 20 SNPs in pooled samples of DNA from 1000 donors. Furthermore we have used these SNPs to genotype blood samples from 112 former breast cancer patients at the Norwegian Radium Hospital, originating from families with several cases of breast cancer combined with an absence of known family mutations. Generated data will be utilized in a linkage analysis. In this way we will examine the possibilities of replicating previous studies that have indicated a linkage between hereditary non-BRCA1/2 breast cancer in Scandinavian populations to chromosome 13q. Per September 2005 we are unfortunately not finished analyzing the data from the genotyping part of the project, hence this paper does not contain results from the linkage analysis.