This update attempts to describe the composition and bioactive substances present in the various by-products generated during the industrialization of fruits and vegetables. Most of the residues originate after juice extraction or the use of fruits and vegetables for other purposes. The inedible parts, outer layers and seeds, are generally discarded in most cases. These residues are quickly subject to degradation and contamination by pathogens. These residues are very rich in bioactive compounds (BA) indicating that even with juice extraction, a considerable amount of BA compounds remain. These compounds exhibit a wide range of antioxidant, antimicrobial, anti-inflammatory, anti-allergic, anti-atherogenic, cardioprotective and vaso-dilatory effects. By-product extracts or isolated compounds can be used as ingredients in functional foods or as nutraceuticals in medicinal or pharmaceutical preparations.