This project focuses on the overall genomic as well as Major Histocompatibility Complex (MHC) diversity and polymorphism in dogs and horses. Extensive breeding for specific traits using closely related individuals has resulted in limited genetic variation in many breeds of dogs and similar phenomenon is underway in horses. The loss of variation leads to increased prevalence of diseases. In some dog breeds, the lack of genetic variation has led to the fixation of certain health problems, such as brachycephalic skull in Mops or mitreal valve disease in Cavallier King Charles Spaniel. Our research focuses on different inherited diseases and we are currently studying the genomic diversity to learn more about the processes that lead to these diseases. A large focus is on the diversity and polymorphism of the MHC region in dogs and horses, because this region has many implications to disease susceptability and outcome.