The consumption of flavonoid-rich foods could have beneficial effects on health. However, different classes of flavonoids have different effect on disease risk and the relationship between flavonoid intake and risk of disease appeared to be non-linear. Furthermore, contrarily to vitamins, there are no symptoms of deficiency for flavonoids; therefore, our body treats them like other xenobiotics. Therefore, a therapeutic index should be determined. Despite flavonoids are at the pharma-nutrition interface, drugs and foods are subject to different regulatory frameworks and there is no recommended daily allowance (RDA) for flavonoids. Relatively little is known about the efficacy, safety and underlying mechanisms of these bioactive compounds, especially when taken in concert with drugs. Flavonoids could act both as drugs and pro-drugs with pharmacological and toxicological promiscuity. Due to the low bioavailability, the gastrointestinal tract could be the primary target of flavonoids and metabolites. Different effects have been observed after acute and chronic consumption and bioavailability and bioactivity have high inter-individual variability. Furthermore, the difficulties in the design and in the interpretation of human intervention studies make difficult the establishment of a therapeutic index for flavonoids. Probably the concept of ‘personalized nutrition’ previously proposed could be the better approach. However, despite more studies are needed in order to establish a therapeutic index for each flavonoid subclasses, at the moment RDA of total flavonoids could be between 250–400mg/d, respecting the seasonality of food sources.