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[Objective] Identification of single nucleotide polymorphisms (SNPs) and candidate genes significantly associated with the content of γ-aminobutyric acid (GABA) in rice grains may provide a theoretical basis for further exploring the molecular mechanism of GABA enrichment in rice grains, and lay the foundation for cultivating high-GABA content varieties. [Method] This study performed genome-wide association studies (GWAS) for GABA content with re-sequencing in 139 early japonica rice core germplasm resources in Northwest China. The candidate genes were screened based on haplotype analysis and gene annotation, and expression pattern of candidate genes were analyzed by expression profile database and fluorescence quantitative PCR. [Result] GABA content in grains showed abundant variation with a coefficient of variation of 31.25%. Genome-wide association analysis showed a total of 6 significant and representative SNPs on chromosomes 6, 8, 9, 11 and 12 were detected, and OsBADH2 and OsGABA-T2, which have been cloned in relation to GABA content. In addition, six candidate genes were predicted for GABA content in the rice grains, among which LOC_Os09g10720 was identified as highlight candidate gene, and the feasibility of its involvement in the decomposition of GABA in rice grains was further verified. [Conclusion] A total of 6 SNPs significantly associated with GABA content in rice grain are detected. And 6 candidate genes that might be associated with GABA content are screened out, they are LOC_Os09g09750, LOC_Os09g09760, LOC_Os09g10210, LOC_Os09g09820, LOC_Os09g10280 and LOC_ Os09g10720. Among them, LOC_Os09g10720 was used as a focus candidate gene. [ABSTRACT FROM AUTHOR]