While brown rice is an efficient source of both phenolics and tocopherols, little is known regarding the WZ4002 genetic basis for the variation in type and quantity of these components in cooked rice across genetically diverse varieties. The functional impact of SNP-derived genetic variation in pathways that regulate the production of dietary bioactive compounds in rice is also unclear. Metabolomics, the comprehensive analysis of low-molecular-weight compounds in biological samples, provides a high-throughput and sensitive approach to assess the outcome of different genotypes on metabolites in the cooked grain. New evidence supports the utility of this technique to capture the complexity of the rice metabolome and to evaluate changes in metabolic responses. However, there has been minimal integration of the rice metabolomic signature with genomic data sets and the use of this information to assess components of dietary importance. A systems biology approach was applied herein to reveal the synthesis and metabolic regulation of nutritionally important phytochemicals, by profiling multiple rice varieties for pathway-specific SNPs with metabolomics. The diversity in genetic and morphological rice traits from the OryzaSNP set was interrogated herein by applying metabolomic analysis to the cooked grain. Previous studies have established metabolite profiles for crop varieties, however metabolites were extracted from raw plant material. The screening of metabolites in cooked rice enhanced the dietary relevance of our findings, as the nutritional differences detected resembles actual metabolite intake following heat and moisture. An open-boiling technique was standardized for this study because of the global utilization of this cooking method. Recent reviews emphasize the need for sustainable, breeding based approaches to enhance plant food nutritional quality. An integrated genomic and metabolomic method has been proposed as a useful measure to improve food crops. A number of studies successfully correlated genomics with metabolomics, such as in the associations of quantitative trait loci with metabolite profiles in Arabidopsis and of restriction fragment length polymorphism markers with nuclear magnetic resonance generated metabolite profiles in uncooked rice. An analysis of SNPs provides a new functional relevance for the differences detected in the rice metabolome. The integration of SNP-based bioinformatics with metabolomics as conducted herein may now be utilized to assist in selection of rice varieties with enhanced nutritional and health-promoting value. The extensive metabolite variation in different varieties of cooked rice was approximately 25% of the total metabolites detected. The z-score analysis using Nipponbare as a reference was a compelling example of the metabolite diversity among the varieties. Z-scores were calculated to determine metabolites that vary between one variety and a reference variety. An excessively high or low z-score usually indicated a metabolite present in one variety and absent in another.