The influence of genotype (selection), location, and year on antioxidant activity (AOA), total phenolics (TP), total carotenoids (TC), phenolic and carotenoid composition was studied using specialty (colored) potatoes (Solanum tuberosum L.) from the Texas Potato Variety Development Program, grown at two Texas locations (McCook and Dalhart), and in two years (2003 and 2004). Chlorogenic acid, gallic acid, catechin, caffeic acid, and malvidin-3-(p-coumaryl rutinoside)–5-galactoside were the major phenolics, and lutein and violaxanthin were the major carotenoids identified. The AOA, TP, and TC and phenolic composition differed significantly with genotype, location and year. However, genotypic effects were larger than location and year effects. Selection CO112F2-2 was high in all the measured parameters and also stable across locations and years, suggesting that this selection could be used as a parent in breeding varieties with improved health benefits. The AOA, TP and chlorogenic acid content were highly significantly correlated with one another. The effects of whole specialty potato extracts, fractions and individual compounds on LNCaP (androgen-dependent) and PC-3 (androgen-independent) prostate cancer cells were also investigated. Ethanol extract of the selection CO112F2-2 (5 µg chlorogenic acid eq/ml), the anthocyanin fraction (AF; 5 µg chlorogenic acid eq/ml), gallic acid and chaconine showed potent anti-proliferative properties and increased the cyclin-dependent kinase inhibitor p27 levels in LNCaP and PC-3 cells. Induction of apoptosis was cell context dependent and associated with JNK (c-Jun NH2-terminal Kinase) and Erk (extracellular signal regulated kinase) activation. Cell death pathways, induced by potato extract and the AF, were associated with Erk and JNK activation, and these kinases activated caspase-independent apoptosis through nuclear translocation of endonuclease G (endo G) and apoptosis-inducing factor (AIF) in both cell lines. Induction of caspase-dependent apoptosis was also kinase-dependent but was observed only in LNCaP cells. Kinase inhibitors reversed this nuclear translocation of endo G and AIF. This is the first report showing that the cytotoxic activities of potato extract/AF in cancer cells were due to activation of caspase-independent apoptosis.