The characterization of Lycopersicon germplasm for internal quality properties is essential to choose suitable donor parents for breeding programs. When donor parents belong to species of subgenus Eulycopersicon, which are phyletically closer to L. esculentum Mill., the recovery of agronomic traits is faster. When using these materials, a careful selection of donor parents which could improve several internal quality properties allows the acceleration of these breeding programs. In this work, we combine general determinations, such as soluble solid content, titratable acidity, pH, total sugars, pectic substances and total protein contents with precise high-performance liquid chromatography (HPLC), quantitations of individual compounds (vitamin C; citric, malic, fumaric and oxalic acids; glucose, fructose, and sucrose), in order to obtain a more complete characterization of flavor intensity and nutritional properties in Lycopersicon germplasm. The multidimensional analysis of all these variables allows classification of several accessions of L. esculentum Mill. and L. pimpinellifolium (Jusl.) Mill., according to their usefulness for internal quality breeding programs of fresh tomato. The classification obtained and the comparison of accessions quality characteristics with selected controls show that five of the L. pimpinellifolium (Jusl.) Mill. accessions tested can be of great usefulness for being used in breeding for internal quality characteristics. A flavor intensity ≈625% higher than commercial hybrids was obtained in the best accession tested. Some of these L. pimpinellifolium (Jusl.) Mill. accessions showed better flavor intensity properties than a high SSC L. cheesmanii Riley control, traditionally used in internal quality breeding. In addition, three of the L. esculentum Mill. accessions tested with medium-to-high flavor intensity value could be useful in advanced stages of breeding programs.