Rice (Oryza sativa) is vital source of calories as a staple food crop, and genetic diversity has been implicated as a source of variation in the quantity of nutritionally important metabolites in the cooked grain. However, the influence of environmental conditions on the metabolite profile of the grain is unknown. Two cultivars of rice, IR64 (advanced line) and Moroberekan (landrace), were grown in a field and greenhouse environment. Rice grain was dehulled, cooked, and lyophilized to remove water. Metabolites were extracted using an aqueous methanol solvent and detected by gas chromatography coupled to mass spectrometry. Mass spectral database matches were used to identify 34 candidate compounds, including amino acids, fatty acids, mono- and disaccharides, inorganic and organic acids, and others. An ANOVA was performed for each metabolite, and genetic, environment, and genetic by environment interactions were observed. A bioinformatics approach that integrated rice genetic and metabolic information was used to explain covariance among metabolites under the two environmental conditions. These results suggest that metabolites are influenced by environmental effects and may determine health properties of the cooked grain.