Research interest on functional food and phytochemicals has mainly focused on their health effects, mechanism of action and structure-activity relationship for the development of nutraceuticals. Considering the intake of phytochemicals via the normal diet, further information is required on changes in food functionality or individual phytochemicals that occur during the cooking or processing of foods, in order to increase the intake of these bioactive compounds, because many of the unit-operating procedures involved in cooking or food processing may result in physicochemical changes of food constituents. This study reviews the changes of selected phytochemicals, i.e. flavonoids, organosulfur compounds and carotenoids, or food functionality by major cooking or processing procedures such as heating, fermentation, and pH changes. In general, heating has a negative effect on food functionality, although in some cases, mild heating increases bioactive phytochemical contents. Some phytochemicals, including anthocyanins and catechins, are stabilized in lower pH conditions. The structures of phytochemicals, including isoflavones and catechins, are changed by fermentation. The loss of bioactive compounds may be decreased by recently developed cooking or processing methods such as microwave cooking or use of high hydrostatic pressure. However, the effects of cooking and processing procedures on food functionality and phytochemicals are so diverse and dependent on test conditions that further research efforts are needed to form accurate conclusions on the effects of cooking and processing of foods.