Tomato fruit quality is determined by the contents of various functional metabolites in addition to fruit appearance. To develop tomato cultivars with higher amounts of functional compounds, an efficient quantification method is required to identify the natural variations in the compounds in the tomato germplasm. In this study, we investigated tomato varieties, which included 23 inbred lines and 12 commercial F 1 cultivars, for their contents of seven watersoluble vitamins (vitamin C, vitamins B1, B2, B3, B5, B6, and B9) and five polyphenolic compounds (quercetin, rutin, kaempferol, myricetin, and naringenin chalcone). The results of high performance liquid chromatography and liquid chromatography-mass spectrometry showed that vitamin C and naringenin chalcone were the major water-soluble vitamins and polyphenolic compounds, respectively, and their abundance was highly variable depending on the cultivar. By contrast, the contents of vitamin B1, quercetin, and kaempferol were lowest among the cultivars. With regard to the relationship between metabolic compounds and fruit characteristics, a significant association was found in fruit size, indicating that cherry tomato varieties contain higher amounts of the compounds compared to large fresh-type varieties. However, no direct association was detected in fruit color, except for naringenin chalcone. The results of this study provide new insights on the quantification of metabolic compounds and the selection of breeding materials, which are prerequisites for the development of functional tomato varieties.