The product categories in which natural compounds can be found as active ingredients include drugs pharmaceuticals, cosmetic ingredients and dietary supplements and natural health product ingredients. Bioactive compounds can be classified according to the following criteria: clinical function; biological effects; botanical categorization; biochemical pathways and chemical classes. The bioactive compounds extracted from winery by-products can be used as medicine due to their antioxidant, antimicrobial, anti-inflammatory and anticancer activities. Waste streams or vegetal by-products obtained from the food and agriculture could be regarded as bio-renewable sources of valuable components for use in the pharmaceutical industry. The reuse of components of by-products and agricultural and food waste can prove a useful tool in increasing the eco-sustainability of food processing industries and to exercise a positive economic impact. Identification of bioactive compounds in plants, microrganisms and animals is a growing field and processing of by-products facilitates commercial applications.