Peel powders from seven commercial cherry and grape tomato varieties (Mini Kumato, Durst Orange, Durst Purple, Orange, Zima, Cherub, and Mini Heirloom) and, for comparison, one industrial potato variety (Umatilla Russet) were analyzed for free amino acid, phenolic, flavonoid, β-carotene, lycopene, and glycoalkaloid content using high-performance liquid chromatography/mass spectrometry (HPLC/MS). The powders were prepared by hand-peeling the tomatoes, freeze-drying the wet peels, and then grinding dry peels to fine powders. The total free amino acid content of the tomato peels was in the range 23.7-57 mg/g, and of the potato peel was 38.0 mg/g, with an essential amino acid content of 9.1-18.0% of the total. The chlorogenic acid content of the Mini Heirloom variety of tomato was several-fold greater than that of the other varieties. The content of the flavonoids rutin and of the quercetin glucosides also varied, as did the β-carotene content; no β-carotene was recorded in two varieties. Lycopene was present in three tomato peels but absent in four. Dehydrotomatine and α-tomatine were not found in six peels but were high in Mini Heirloom. The analytical method could be used to determine two tomato (dehydrotomatine, α-tomatine) and two potato (α-chaconine, α-solanine) glycoalkaloids in a single assay. Food processors and consumers might be able to select cherry tomato varieties with peels containing the highest amount of the evaluated compounds, all of which have been reported to have health benefits.