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To evaluate the incidence of loss of heterozygosity (LOH) and microsatellite instability (MI) in pterygia and their possible correlation with clinical variables.50 pterygia, blood, and conjunctival specimens were obtained. A personal and family history was recorded for each patient. Amplification of 15 microsatellite markers at regions 17p, 17q, 13q, 9p, and 9q was performed using the polymerase chain reaction. The electrophoretic pattern of DNA from pterygia was compared with the respective pattern from blood and conjunctiva.LOH incidence was the highest at 9p (48%), followed by 17q (42%). Only three cases displayed MI. LOH incidence at individual markers was positively correlated with recurrence (D9S59, p=0.11 and D9S270, p=0.16), family history of neoplasia (D13S175, p=0.09), altitude of present residence (D9S112, p=0.1), duration of the existence of pterygium (D9S144, p=0.06), and inversely correlated with age (D9S59, p=0.09). Concerning chromosome arms, LOH was positively correlated with the altitude of present residence (13q and 17p, p=0.03) and duration of the existence of pterygium (13q and 17p, p=0.09).LOH is a common event whereas MI is a very uncommon one at the examined markers in pterygium, indicating the presence of putative tumour suppressor genes implicated in the aetiopathogenesis of the disease. The fact that LOH at 9q31-33 was more frequent in recurrent pterygia and also correlated with known risk factors such as young age and high altitude of residence, implies a possible predictive value of this finding for postoperative recurrence.