In the presence of transition metal ions and peroxides, polyphenols, well-known dietary antioxidants, can act as pro-oxidants. We investigated the effect of 13 polyphenols and their metabolites on oxidative degradation of deoxyribose by an •OH generating Fenton system (Fe2+-ethylenediaminetetraacetic acid (EDTA)-H2O2). The relationship between phenolics pro-oxidant/anti-oxidant effects and their molecular structure was analyzed using multivariate analysis with multiple linear regression and a backward stepwise technique. Four phenolics revealed a significant inhibitory effect on OH-induced deoxyribose degradation, ranging from 54.4% ± 28.6% (3,4-dihydroxycinnamic acid) to 38.5% ± 10.4% (catechin) (n = 6), correlating with the number of –OH substitutions (r = 0.58). Seven phenolics augmented the oxidative degradation of deoxyribose with the highest enhancement at 95.0% ± 21.3% (quercetin) and 60.6% ± 12.2% (phloridzin). The pro-oxidant effect correlated (p < 0.05) with the number of –OH groups (r = 0.59), and aliphatic substitutes (r = −0.22) and weakly correlated with the occurrence of a catechol structure within the compound molecule (r = 0.17). Selective dietary supplementation with phenolics exhibiting pro-oxidant activity may increase the possibility of systemic oxidative stress in patients treated with medications containing chelating properties or those with high plasma concentrations of H2O2 and non-transferrin bound iron.