A diverse array of fruit and vegetable constituents including vitamins such as C, E and A, phytochemicals such as folates, glucosinolates, carotenoids, flavonoids and phenolic acids, lycopene, selenium and dietary fibres form an antioxidant network that is essential in maintaining human health. In two apple cultivars, we showed that flavonoids are stable after harvest and there were no losses during storage in air and controlled atmosphere (CA) conditions and during shelf life. Thus the health benefits of phenolics in apples should be maintained during long-term storage. However, more research is required to evaluate the effects of storage conditions and post-harvest handling on the retention of other health-related compounds in fruits and vegetables.