Epidemiological studies have indicated that the consumption of fruits and vegetables is associated with a reduced risk for the development of chronic diseases, such as cardiovascular disease and cancer. Phytochemicals, including phenolics and flavonoids, are suggested to be the major bioactive compounds contributing to the health benefits of fruits and vegetables. Onions are a major source of dietary flavonoids; however, there may exist varietal differences in composition, concentration, and beneficial activities. To characterize these differences, shallots and 10 onion (Allium cepa L.) varieties commonly available in the United States (Western Yellow, Northern Red, New York Bold, Western White, Peruvian Sweet, Empire Sweet, Mexico, Texas 1015, Imperial Valley Sweet, and Vidalia) were evaluated for total phenolic and flavonoid contents and antioxidant and antiproliferative activities. Shallots contained the highest total phenolic content (114.7 +/- 10.0 mg/100 g of sample) among the varieties tested, with a 6-fold difference observed when compared to the variety with the lowest phenolic content (Vidalia, p < 0.05). Western Yellow onion variety exhibited the highest total flavonoid content (69.2 +/- 3.7 mg/100 g of onion) of the varieties tested, with an 11-fold difference when compared to the variety with the lowest flavonoid content (Western White, p < 0.05). Shallots exhibited the highest total antioxidant activity (45.5 +/- 2.1 micromol of vitamin C equiv/g of onion), followed by Western Yellow, New York Bold, Northern Red, Mexico, Empire Sweet, Western White, Peruvian Sweet, Texas 1015, Imperial Valley Sweet, and Vidalia. For all varieties, both total phenolic and flavonoid contents were strongly correlated with total antioxidant activity (R (2) = 0.9668, p < 0.05; and R (2) = 0.7033, p < 0.05, respectively). The proliferation of HepG(2) and Caco-2 cells was significantly inhibited in a dose-dependent fashion after exposure to the Western Yellow, shallots, New York Bold, and Northern Red extracts, with Western Yellow, shallots, and New York Bold exhibiting the highest antiproliferative activity against HepG(2) cells and New York Bold and Western Yellow exhibiting the highest antiproliferative activity against Caco-2 cells. However, the varieties of Western White, Peruvian Sweet, Empire Sweet, Mexico, Texas 1015, Imperial Valley Sweet, and Vidalia demonstrated weak antiproliferative activity against both HepG(2) and Caco-2 cells. These results may influence consumers toward purchasing onion varieties exhibiting greater potential health benefits and may significantly affect future breeding efforts to enhance onion nutritional qualities.