A Belgian population of ten breeds with a low to moderately low genetic diversity or which are relatively popular in Belgium, i.e. Bichon frise, Bloodhound, Bouvier des Flandres, Boxer, Cavalier King Charles spaniel, Irish setter, Papillon, Rottweiler, Golden retriever and Labrador retriever, was genotyped for all potentially relevant disease-causing variants known at the start of the study. In this way, the frequency was estimated for 26 variants in order to improve breeding advice. Disorders with a frequency high enough to recommend routine genotyping in breeding programs are (1) degenerative myelopathy for the Bloodhound, (2) arrhythmogenic right ventricular cardiomyopathy and degenerative myelopathy for Boxers, (3) episodic falling syndrome and macrothrombocytopenia for the Cavalier King Charles spaniel, (4) progressive retinal atrophy rod cone dysplasia 4 for the Irish setter (5) Golden retriever progressive retinal atrophy 1 for the Golden retriever and (6) exercise induced collapse and progressive rod-cone degeneration for the Labrador retriever. To the authors’ knowledge, in this study, the presence of a causal mutation for a short tail in the Bouvier des Flandres is described for the first time.