Abstract: A method is disclosed for identifying genetic markers associated with desirable and undesirable traits in horses, including athletic performance, physical structure, injury susceptibility, and disease susceptibility. The method involves partial sequencing of the horse genome, polymorphism identification, and whole-genome linkage analysis. When identified, these markers are utilized to create assays for inherited predisposition of a horse toward important physical traits and disease. The present invention also relates to a method of predicting desirable and undesirable traits in horses utilizing genetic markers of the present invention.