A recent genome-wide association study (GWA) reported a significant association between single nucleotide polymorphisms (SNPs) at the PCDH11X gene and late-onset Alzheimer's disease (LOAD). Our research was designated to replicate this association, including non previously analyzed PCDH11X and PCDH11Y SNPs. We genotyped four PCDH11X and one PCDH11Y SNPs in a total of 420 LOAD patients and 350 healthy controls from Spain. Allele and genotype frequencies did not differ between patients and controls for the five SNPs, even after correcting by gender, age, and APOE-ε4 status. Our data were in agreement with recent reports that failed to confirm the association between PCDH11X polymorphisms and LOAD, and extended the lack of association to common PCDH11Y variants.