The levels of somatostatin are consistently decreased in the brain and cerebrospinal fluid of Alzheimer's disease (AD) patients. The somatostatin gene is located on chromosome 3q27.3 close to an association region identified in late-onset AD patients originating from Finland. Since somatostatin is a good candidate on both positional and functional grounds, we studied whether single nucleotide polymorphisms (SNPs) in the somatostatin gene were associated with AD in the Finnish population. We genotyped three SNPs within this gene in Finnish AD patients (n = 424) and non-demented controls (n = 466). AD patients were compared with non-demented control subjects using single-locus and haplotype approaches. In the whole study group, the age, sex and APOE adjusted OR for the risk of AD in C-allele carriers of the SNP rs4988 514 was 1.42 (p <0.05). Interestingly, in APOE epsilon4-allele carriers, the age and sex adjusted OR for the risk of AD in C-allele carriers of the rs4988 514 increased to 2.05 (p <0.01). Additionally, SNP rs4988514 may interact with the APOE epsilon4-allele to increase the risk of AD. Assessment of individual haplotype distributions revealed a 2-fold overrepresentation of the TCG haplotype of SNPs rs3864101, rs4988 514 and rs7624 906 in the AD APOE epsilon4-allele group (p <0.01). Conversely, a major haplotype TTG was significantly underrepresented among all the AD patients as well as APOE epsilon4-allele carrying AD patients. Thus the major haplotype TTG of somatostatin may have a protective effect against AD. This first genetic association study between somatostatin and AD indicates that genetic variations in the somatostatin gene may modify the risk for AD among Finnish AD subjects.