N-methyl-d-aspartate (NMDA) receptor plays a crucial role in learning, memory and information processing of human brain. Its dysfunction is related to the pathogenesis of Alzheimer's disease (AD). We detected four polymorphisms of the promoter regions of the human NMDA receptor 2B (NR2B) subunit gene (GRIN2B) in 362 AD patients and 334 healthy in North Han Chinese populations, these were -200T/G (rs1019385), -421C/A (rs3764028), -1447T/C (ENS10557853), and -1497G/A (rs12368476). Genetic analysis confirmed that there were significant differences in genotype (P=0.029) and allele (P=0.010) frequencies for -421C/A between SAD and control. In the subjects without APOE varepsilon4 allele, these difference remained significant (genotype P=0.012, allele P=0.004). The -421CC genotype was about 1.5 fold increasing risk compared with CA+AA genotypes (OR=1.517, 95% CI 1.077-2.137, P=0.017). Luciferase reporter assay showed a 34.69-39.79% decrease in transcriptional activity for -421C allele of GRIN2B promoter compared with -421A in SH-SY5Y and HeLa cell lines. Our study suggests that the -421C allele may induce lower GRIN2B transcriptional activity and NR2B protein expression, thus it is associated with AD.