The present number of STR loci adopted in relationship testing is chiefly limited to unlinked markers, in most cases residing on different chromosomes. In order to solve more complex cases of relatedness, e.g. deficient paternities and disputed sibships, the number of core loci can be extended. The inclusion of multiple loci on the same chromosome will, however, increase the risk of possible linkage between markers. We present a new software, FamLink, freely available from http://www.FamLink.se, that can perform statistical calculations based on pedigree structures and account for linkage between pairs of markers. In addition, FamLink can simulate genotype data in order to study the effect of accounting for linkage or not. We demonstrate the importance of taking linkage properly into account using examples and real cases.