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Germinated rice is popularly consumed for its high gamma-aminobutyric acid (GABA) and bioactive compounds. Supporting information on how to germinate rice with high GABA content and essential amino acids is lacking. White and colored rough rice were germinated for 0, 24, 48, 72, 96, 120 and 144 h. GABA, GABA substrates and essential amino acids were also investigated using GC-MS and MALDI-MSI. GABA was more concentrated after germination and shifted into the coleoptile. High correlation was recorded between germination time and GABA (0.79–0.83, p ≤ 0.01) and glutamic acid (0.88–0.89, p ≤ 0.01). Highest rates of GABA and glutamic production were observed within 48 h of germination in both rice varieties (26.12 and 34.28 mg/100g) and reached maximum value at 96 h (31.36 and 38.75 mg/100g). Colored rice germination showed higher GABA, GABA substrates and deficient amino acids …