Although rice has been cultivated as a major food crop for approximately 5,000 years, the interest of customers in ‘scented rice’ is a recent trend in the Korean market. As a part of developing a germinated scented rice variety, the newly bred scented rice variety ‘Cheonjihyang-1 se’ was germinated for 24 h, and changes in profiles of flavor-related volatiles, lipophilic phytonutrients, and fatty acids were investigated. The profiling of volatile compounds by using a headspace-gas chromatography-mass spectrometry (HS-GC-MS) revealed a total of 56 odor-active flavoring compounds; 52 at the pre-germination stage, 51 at the post-germination stage, and 47 common at both stages. The major flavoring compounds were nonanol and benzene, which constituted 11.5% and 6.6%, respectively, of the total peak area in pre-germinated rice, and 19.4% and 6.5%, respectively, in post-germinated rice. Germination induced an increase in 13 flavoring compounds, including 3,3,5-trimethylheptane and 1-pentadecene, which increased by 763 and 513%, respectively by germination. However, we observed a germination-induced decrease in most of the other flavoring compounds. Especially, the most important scented rice-specific popcorn-flavoring compound, 2-acetyl-1-pyrroline, showed 89% decrease due to germination. Furthermore, the germination of scented rice induced a decrease in the content of various phytonutrients. For example, the total contents of phytosterols, squalene, and tocols decreased from 207.97, 31.74, and 25.32 μg g -1 at pre-germination stage down to 136.66, 25.12, and 17.76 μg g -1 , respectively at post-germination stage. The fatty acid compositions were also affected by germination. The composition of three major fatty acids, linoleic, oleic, and palmitic acids, increased from 36.6, 34.2, and 24.4%, respectively, at the pre-germination stage to 37.9, 36.9, and 20.7%, respectively, at the post-germination stage. All these results suggested significant changes in the flavor-related compounds and phytonutrients of the scented rice variety ‘Cheonjihyang-1 se’ during the process of germination, and subsequently the need for developing a more precise process of germination to enhance the flavor and nutritional quality of the germinated scented rice products.