The present invention aims to develop transgenic rice that produces high levels of flavonoids in the entire endosperm. A rice variety, Oryza sativa japonica cv. Hwa-Young, is transformed with maize C1 and R-S genes that together activate most structural genes in the flavonoid biosynthetic pathway. Expression of the C1 and R-S transgenes is endosperm-specific for using the promoter of a 13-kD rice prolamin gene that specifically expresses throughout the endosperm. With variation in pigmentation among 27 independent C1/R-S transgenic lines, the T1 kernels of most lines are light brown and apparently darker than kernels of the wild type as well as rice plants transformed with vector alone. The T2 and T3 kernels of homozygous transgenic lines become darker in pigmentation and smaller in size than T1 kernels.