Markers have been used for some time to study the genetic control of economically important traits in livestock. The early work was based on single loci and detected some significant effects, but results were often inconsistent across studies. Now that complete microsatellite-based maps of the major species are becoming available, more complete and rigorous scans of the genome are possible. The first of these have detected some surprisingly large effects, both within breeds and in breed crosses. As research workers digest these results and their implications for livestock breeding programmes and ponder further research, commercial breeding companies have already started applying the first fruits of marker research to breed a better animal.