Advances in molecular genetics have opened opportunities to enhance strategies for genetic improvement of livestock by directly selecting on genes or chromosomal regions that harbor genes that affect traits of interest, so-called quantitative trait loci (QTL). Detection and use of QTL relies on presence of linkage disequilibrium between genetic markers that can be genotyped and QTL. The nature of linkage disequilibrium that exists in populations or that can be created in experimental populations and its use in QTL detection and marker-assisted selection are reviewed. Limitations and opportunities for alternate strategies for marker-assisted selection are outlined. The main conclusion is that opportunities for use of marker-assisted selection to enhance rates of genetic improvement exist, in particular using population-wide disequilibrium, but they require careful analysis and implementation in existing breeding programs.