Abstract Background Selective breeding in populations with a limited effective population size may result in a loss of genetic diversity, which can cause an increased concentration of specific disease liability genes. The Dutch Shepherd Dog (DSD) in the Netherlands is an example of such a breed with a small effective population. Objective To evaluate the measurement of genetic diversity and multiplex DNA panel screening for implementation in a breeding strategy for the Dutch Shepherd Dog (DSD) and to investigate the clinical relevance of potentially identified mutations in the multiplex DNA panel screening. Results Genome-wide SNP testing showed genetic isolation and reduced genetic diversity within coat variety subgroups of the DSD. Panel screening identified a Von Willebrand’s Disease type I mutation. Although decreased Von Willebrand’s Factor proteins were significantly lower in DSDs carrying the VWD-I allele compared to the wildtype, clinical follow-up did not show a significant association between the clinical phenotype and VWD-I genotype. Conclusions Genetic relationship measurement within a breed population may be a useful tool to enable breeding strategies to conserve genetic diversity. Results from a disease panel screening need to be evaluated for clinical relevance before breed selection restrictions can be considered.