Increased consumption of fruits and vegetables has been associated with risk reduction for cancer. The protective effects by these plant-based foods have been ascribed to the presence of polyphenols, which comprise a complex class of bioactive food compounds. Dietary polyphenols have been shown to exert several nutrigenomics actions by modulating several metabolic, cellular and molecular processes involved in cancer prevention, although the exact mechanisms remain unknown. Metabolomics represents a promising analytical approach for the investigation of large sets of metabolites in plasma, urine and feces. Metabolomics approaches have provided insight on key aspects related to dietary polyphenols’ nutritional effects, including intake estimation, bioavailability and biological actions. It is anticipated that the integration of metabolomics with other “omics”, including transcriptomics and proteomics, in a systems biology perspective will contribute to the definition of consistent dietary recommendations focusing on polyphenol consumption for health promotion and cancer prevention.