Plants are one of the most important resources of human foods and medicines. Rapidly increasing knowledge on nutrition, medicine, and plant biotechnology has dramatically changed the concepts about food, health and agriculture, and brought in a revolution on them. Nutritional therapy and phytotherapy have emerged as new concepts and healing systems have quickly and widely spread in recent years. Strong recommendations for consumption of nutraceuticals, natural plant foods, and the use of nutritional therapy and phytotherapy have become progressively popular to improve health, and to prevent and treat diseases. With these trends, improving the dietary nutritional values of fruits, vegetables and other crops or even bioactive components in folk herbals has become targets of the blooming plant biotechnology industry. This review attempts to display and remark on these aspects. It summarizes the progress made on nutraceuticals, nutritional therapy, phytonutrients, phytotherapy, and their related epidemiological investigations and clinical studies. It also covers markets of these health-promoting products and disease-preventing or healing systems, as well as regulations behind them that direct the development of biotechnology study and application. Finally, related patents are listed and briefly analyzed, regarding of plant biotechnological research and progress on transgenic crops to improve nutritional value, phytotherapy efficiency, or to produce pharmaceutically important secondary metabolites or high-valued protein medicines such as vaccines and antibodies.