<title>Abstract</title>Alzheimer’s disease (AD) has no cure, but early detection and risk prediction could allow earlier intervention. Genetic risk factors may differ between ethnic populations. To discover novel susceptibility loci of AD in the Japanese population, we conducted a genome-wide association study (GWAS) with 3962 AD cases and 4074 controls. Out of 4,852,957 genetic markers that passed stringent quality control filters, 134 in nine loci, including <italic>APOE</italic> and <italic>SORL1</italic>, were convincingly associated with AD. Lead SNPs located in seven novel loci were genotyped in an independent Japanese AD case–control cohort. The novel locus <italic>FAM47E</italic> reached genome-wide significance in a meta-analysis of association results. This is the first report associating the <italic>FAM47E</italic> locus with AD in the Japanese population. A trans-ethnic meta-analysis combining the results of the Japanese data sets with summary statistics from stage 1 data of the International Genomics of Alzheimer’s Project identified an additional novel susceptibility locus in <italic>OR2B2</italic>. Our data highlight the importance of performing GWAS in non-European populations.