To explore the association between single nucleotide polymorphisms (SNPs) in Pen2 gene and late onset Alzheimer's disease (LOAD) in North Chinese population.The genotypes of ApoE and Pen2 gene were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and direct sequencing respectively in 480 LOAD patients and 480 healthy controls. The strength of association between polymorphisms and AD was estimated with odds ratios (OR).The genotype of IVS2 + 335T < A was obtained. There was an association between IVS2 + 335T < A and apolipoprotein E (ApoE) genotypes (P = 0.002). In the subjects with APOEε 4 allele, there were significant differences in the distribution of alleles (P = 0.003) and genotypes (P = 0.007) between AD and control groups. The ORs (95% confidence interval (CI)) of allele A and T/A + A/A genotypes were 4.720 (1.517 - 10.654) and 3.886 (1.381 - 10.932) respectively with allele T and genotype T/T as references.An association exists between IVS2 + 335T < A and the development of LOAD in ApoEε 4 carriers within the northern Chinese population. And allele A of Pen 2 gene may increase the risk for LOAD.