Abstract. Since the beginning of investigation in the horse genome in the early nineties, there has been a great progress, especially during the last five years. At the beginning the exploration of monogenic hereditary diseases was one of the main aims, and the causal mutations of several diseases in the horse have been unravelled. The inheritance of coat colours has been explored very detailed, and there exist gene tests for different coat colours. Information about coat colours and inherited diseases is very important for the breeders and helps avoiding the appearance of lethal genetic factors or undesirable diseases. The most important achievements of horse genome analysis were well-developed linkage, radiation hybrid and cytogenetic genome maps including more than 2950 loci. These maps support comparative analysis of equine hereditary diseases. The present known gene mutations for five diseases in horses have human homologs. Studies on multifactorial diseases such as osteochondrosis and navicular bone disease and on fertility and temperament are underway. At the moment, the whole equine genome is sequenced as it has been done for the human genome and also for other animal genomes. Horse breeding will greatly benefit from identification of QTL for multifactorial traits and gene mutations for congenital anomalies, diseases and performance traits.