In tomato, Lycopersicon esculentum Mill., currently there are more than 285 known morphological, physiological and disease resistance markers, 36 isozymes and over 1000 restriction fragment length polymorphisms (RFLPs), which have been mapped onto the 12 tomato chromosomes. In addition, currently there are over 162,000 expressed sequence tag (EST) markers, of which ~3.2% have been mapped. Several tomato genetic maps have been developed, mainly based on interspecific crosses between the cultivated tomato and its related wild species. The markers and maps have been used to locate and tag genes or QTLs for disease resistance and many other horticultural characteristics. Such information can be used for various purposes, including marker-assisted selection (MAS) and map-based cloning of desirable genes or QTLs. Currently, MAS is adopted by many seed companies for manipulating genes controlling vertical resistance to tomato diseases such as bacterial speck, corky root, fusarium wilt, late blight, nematodes, powdery mildew, tobacco/tomato mosaic virus, tomato spotted wilt virus, tomato yellow leaf curl virus, and verticillium wilt. However, for seed companies, MAS is not yet a routine procedure for manipulating QTLs in tomato, although it has been tried to improve bacterial wilt, bacterial canker and tomato yellow leaf curl virus as well as for improving fruit soluble solids (°Brix). In comparison, the use of MAS is generally less common in public tomato breeding programs although attempts have been made to transfer QTLs for resistance to blackmold and late blight as well as for some fruit quality characteristics. The potential benefits of marker deployment to plant breeding are undisputed, in particular for pyramiding disease resistance genes with different gene actions or pathogen specificity. It is expected that in the near future MAS will be routine in many breeding programs, taking advantage of high-throughput and high-resolution markers such as single-nucleotide polymorphisms (SNPs). For quantitative traits, QTLs must be sought for components of genetic variation before they are applicable to marker-assisted breeding. However, MAS will not be a "silver bullet" solution to every breeding problem or to every crop species.