Previous studies have demonstrated that clusterin (CLU), which is also known as apolipoprotein J, is involved in the pathogenesis of Alzheimer disease (AD). In this study, we investigated the association between rs2279590, rs11136000, and rs9331888 single-nucleotide polymorphisms (SNPs) in CLU and apolipoprotein E (APOE) genotypes in a cohort of Turkish patients with late-onset AD (LOAD). There were 183 patients with LOAD and 154 healthy controls included in the study. The CLU and APOE polymorphisms were genotyped using the LightSNiP assay. The GG genotype of rs9331888 was significantly more frequent in patients with LOAD. The CC genotype of the SNP was significantly more frequent in controls. The rs9331888 GG genotype in patients and the CC genotype in controls were significantly higher in non-4 allele carriers of APOE. The haplotype analysis showed the CLU GCG haplotype was a risk haplotype. Our findings indicate the rs9331888 SNP of CLU is associated with LOAD independent of APOE.