We investigated insertion (Ins)/deletion(Del) polymorphism in alpha-2-macroglobulin (A2M), G/C variant in the beta-site amyloid precursor protein-cleaving enzyme 1 (BACE1) and apolipoprotein E (APOE) gene epsilon2/epsilon3/epsilon4 polymorphism in 387 Chinese Han ethnic patients with Alzheimer's disease and healthy study participants. After stratification for APOEepsilon4 status, only the BACE1-G allele with APOEepsilon4 was significantly associated with Alzheimer's disease. Through meta-analysis of the Del or G allele by pooling Asian studies, only BACE1-G allele appeared to increase risk of developing Alzheimer's disease. Through combination-analysis of the data about the A2M-I/D and the A2M-Ile1000Val variants, the A2M gene was suggested to be associated with Alzheimer's disease.