A metabolite profiling approach based on gas chromatography-mass spectrometry (GC-MS) was used to investigate time-dependent metabolic changes in the course of the germination of rice. Brown rice kernels were soaked and incubated for a total of 96 h under ambient conditions. Samples taken during the germination process were subjected to an extraction and fractionation procedure covering a broad spectrum of lipophilic (e.g., fatty acid methyl esters, hydrocarbons, fatty alcohols, sterols) and hydrophilic (e.g., sugars, acids, amino acids, amines) low molecular weight rice constituents. Investigation of the obtained fractions by GC resulted in the detection of 615 distinct peaks, of which 174 were identified by means of MS. Statistical assessment of the data via principal component analysis demonstrated that the metabolic changes during the germination process are reflected by time-dependent shifts of the scores, which were similar for the three rice materials investigated. Analysis of the corresponding loadings showed that polar metabolites were major contributors to the separation along the first principal component. Relative quantifications based on standardized peak heights revealed dynamic changes of the metabolites in the course of the germination.