The content of total polyphenols, chlorogenic, caffeic (CaA) and ferulic acids, and rutin, was investigated in plant organs of three introgression lines (IL7-3, IL10-1 and IL12-4) of Solanum pennellii in Solanum lycopersicum cv M82 and compared with that of cropped parental. Such study aims to evidence factors associated to the introgressions that can affect polyphenol distribution in plant. Among genotypes few differences in polyphenols were recorded on fresh weight basis. IL7-3 showed higher total polyphenols in fruits and lower rutin in leaves than the other genotypes. IL12-4 showed an increasing trend of total polyphenol concentration in fresh vegetative organs; however, this seems to depend on the lower water content rather than on a higher polyphenol biosynthesis in the genotype. IL10-1 sowed higher CaA and lignin contents in leaves. Such differences agree with the morphological and physiological traits of the genotypes.