Consumers are dissatisfied with the flavor of modern commercial tomatoes; however, modern tomato varieties have many desirable agronomic traits such as shelf life, disease resistance and yield. The flavor deficiency in modern tomatoes is due to a cumulative loss of superior alleles affecting flavor volatiles while breeding for other traits. The lack of breeder focus on the consumer is largely due to the genetic complexity of the tomato flavor phenotype as well as a lack of a simple assay that can define consumer preferences. Tomato flavor is a result of interactions between sugars, acids and aroma volatiles, with volatile compounds giving the tomato fruit its characteristic aroma and flavor. We have quantified 68 flavor biochemicals in over 700 tomato varieties, including modern, heirloom and ancestral tomato accessions. Over 160 of these varieties were evaluated by a large consumer panel for fruit flavor quality traits including overall liking. Genome Wide Association Studies (GWAS) identified genetic loci associated with altered levels of acids, sugars and aroma volatiles. We have used marker-assisted breeding to introgress loci associated with flavor biochemical levels from heirloom varieties into modern tomato varieties. Introduction of seven flavor loci affecting a variety of flavor volatiles into a modern tomato variety has resulted in altered flavor volatile profiles and improved flavor as assessed by a consumer panel.