Phytochemicals including vitamins, carotenoids and phenolic compounds have been widely accepted as the functional substances that make cereal grain health beneficial. Increasing evidence has shown the relation between these antioxidant phytochemicals and reduced risks of oxidative-stress related chronic diseases, such as cardiovascular disease, diabetes and some cancers. Among these cereal grains, rice is of critical importance in agriculture, because of its wide consumption over the world. To breed functional rice with elevated level of phytochemicals, understanding the genes that manipulate the expression of these traits is necessary. This study aims to investigate the genetic bases of phytochemical content in relation to antioxidant properties through the use of association mapping. In other words, the genes that control the levels of phytochemicals in whole rice grains will be identified and related to antioxidant activities. Samples investigated in this study will include yellow, red, purple and black rice, and white rice is used as a control. This study will provide genetic information to improve the health-beneficial properties of rice if marker-assisted selection of breeding is used.