Pseudoexfoliation (PEX) syndrome is characterized by the accumulation of a material of unknown origin in the anterior structures of the eye. Loss of heterozygosity (LOH) in a genetic locus indicates the presence of a gene located in the same region that could be implicated in the development or the progression of a disease. In this study, the occurrence of LOH in tissues involved in PEX and the possible correlation of LOH incidence with clinical parameters were evaluated.Twelve iris specimens, 12 anterior capsule specimens, and respective blood samples were obtained from 17 patients with PEX (13 men), who were undergoing glaucoma and cataract surgery. Sixteen anterior capsule specimens and four iris specimens were obtained from 16 patients without PEX. Polymerase chain reaction was used to amplify 10 highly polymorphic microsatellite markers located on chromosomes 1, 7, 9, and 13.Overall, 83.3% (20/24) of PEX specimens and 94.11% (16/17) of patients with PEX had LOH. The highest incidence of LOH was observed in marker D13S175 (41.6%) followed by D7S478 and D7S479 (37.5%). Only three non-PEX specimens displayed LOH. The number of loci lost was directly related to the altitude of the patients' present residence, but the number lost did not differ significantly between the iris and capsule samples.The occurrence of LOH in tissues involved in PEX implies a genetic role in PEX pathogenesis at a cellu lar level. The correlation of LOH incidence with the altitude of the patient's residence, could indicate an increased susceptibility to UV radiation of the chromosomal regions examined.