Apolipoprotein E (apo E) is directly involved in the amyloid deposition and fibril formation and is present in many cerebral and systemic amyloidoses immunologically. It is encoded by a polymorphic gene and it has three common alleles-epsilon2, epsilon3, and epsilon4. Exfoliation syndrome (XFS) is characterized by the deposition throughout the body of focal fibrillogranular aggregates in which there have been some reports of amyloid or amyloid-like features. We evaluated the possible association between apo E polymorphism and the occurrence of XFS. Using High Pure PCR Template Preparation Kits, genomic DNAs were extracted from whole blood and apo E polymorphisms were determined by using Lightcycler-Apo E Mutation Detection Kits in 76 patients with XFS and 74 controls. The E2/E2, E2/E3 and E2/E4 genotypes (OR 29.9, 95% CI 3.1-293.7; OR 56.1, 95% CI 12.5-252.7; OR 43.9, 95% CI 7.4-257.6, respectively) and the in2 allele are found to have an increased risk of developing XFS (p=0.0001); whereas the in3 allele was found to be protective (p=0.0001). Apo E polymorphism and the presence of in2 allele are seem to be significantly associated with the development of XFS.