Technical Abstract: Emerging evidence supports that cooked brown rice (Oryza sativa L.) contains metabolites with biomedical activities, yet little is known about the genetic diversity that is responsible for metabolite variation and differences in health beneficial traits. Metabolites from cooked brown rice of ten diverse varieties were detected using ultra performance liquid chromatography coupled to mass spectrometry. A total of 3,097 compounds were detected, of which 25% differed among the ten varieties. Multivariate analyses of the metabolite profiles showed that the chemical diversity among the varieties cluster according to their defined subspecies classifications: indica, japonica, and aus. Metabolite-specific genetic diversity in rice was investigated by analyzing a collection of single nucleotide polymorphisms (SNPs) in genes from biochemical pathways of nutritional importance. Nonsynonymous SNPs and SNPs in 5’ and 3’ untranslated regions were found in genes of the phenolics and tocopherol/tocotrienol biosynthesis pathways. Total phenolics and tocopherol concentrations were determined to examine the relationship with the genetic diversity found in the ten varieties. Per gram of cooked brown rice, total phenolics ranged from 113.7 to 392.6 mg (gallic acid equivalents), and total tocopherols ranged between 7.2 and 20.9 mg. These results demonstrate that SNP-based genetic diversity is associated with nutritional components in cooked brown rice and that SNP markers may offer an approach for rice improvement strategies for plant and human health.