The content of two biologically active phenolic compounds (caffeic and chlorogenic acids), two flavonoids (quercetin glucoside and quercetin rutinoside), and two glycoalkaloids (dehydrotomatine and α-tomatine) in green, red, and yellow tomato peels, tomato leaves, and tomato stems harvested from a growing tomato plant was determined by validated high performance liquid chromatography (HPLC) methods. Validation included determining chromatographic properties of commercial standards, hydrolysis of the two glycosides to quercetin, and isolation of the pure glycoalkaloids from a commercial tomatine mixture by preparative chromatography. Analyses of test samples were carried out using fine powders. These were prepared by hand peeling the tomatoes with a knife followed by freeze-drying of the wet peels and then grinding with coffee grinder. The leaves and stems were also freeze-dried and ground to powders. We found extensive variability in the levels of the evaluated compounds. The green tomatoes contained the highest amount of chlorogenic acid, the tomato leaves had the highest amount of quercetin rutinoside (rutin), and the tomato leaves had the highest amount of individual and total glycoalkaloids. The α-tomatine/dehydrotomatine ratio ranged from 1.45 (tomato leaves), to 1.73 (tomato stems), and 4.57 (green tomato peel). The red and yellow tomato peels did not contain measurable amounts of the two glycoalkaloids. The described methods could be used to determine the compositions of the three classes of bioactive compounds in other tomato varieties, the levels of which might be affected by soil and environmental factors and post-harvest storage conditions. Such studies might facilitate further investigations into the relationship between the compositions to the multiple health benefits of the compounds leading to the possible use of tomato powders with the highest content of bioactive compounds as functional food additives.