In times of climate change, growing world populations, and with clear evidence of the depletion or damage to critical resources, it is imperative to take action to sustain and develop the capacity of agricultural and manufacturing systems to continue to provide food, the most basic of human needs. Functional foods, generally defined as foods that provide benefits beyond basic nutrition, represent an important growth category for the commercial sector in many countries around the world. Because of widespread concerns about risks to health, the public is vulnerable to messages about potential health protective advantages of foods formulated in response to emerging nutrition science. This paper argues that it is important to finds ways to evaluate the effects of innovation in this sector. Now more broadly defined, the concept of sustainability provides guidelines for decision-making and a framework for assessing the impact of the development of functional foods as a health protective panacea for diet-related human health problems. However, this paper concludes that when criteria for sustainable practice are applied, there are some strong arguments in support of delaying investment in the development and promotion of functional foods to the general public.