AIMS/BACKGROUND: Pterygium is a common benign lesion of the corneoconjunctival limbus. Although environmental factors, such as ultraviolet irradiation, have been suggested as the main causative factor in the development of the disease, however, the aetiopathology of pterygium remains obscure. In this study the possibility of detecting genetic alterations in the microsatellite DNA of the pterygium was investigated. METHODS: Fifteen specimens were assessed for for loss of heterozygosity (LOH) and microsatellite instability (MI) by seven microsatellite markers on four chromosomal arms. RESULTS: Nine (60%) pterygia exhibited genetic alterations. Eight specimens (53%) exhibited LOH, while two specimens (13%) MI in at least one marker. 17q11.2-q21 is a commonly deleted region, as the frequency of LOH at this region is significantly high (47%). CONCLUSION: This finding indicates the existence of tumour suppressor genes in this region implicated in the disease without excluding the presence of other tumour suppressor genes in the other chromosomal regions that were examined. MI was apparent in only a few specimens but it is indeed a detectable phenomenon, suggesting that decreased fidelity in DNA replication and repair may be associated with the development of pterygium. Detection of LOH and MI, two events taking place in tumour cells or in premalignant cells, constitutes strong evidence that there must be transformed cells in the pterygial tissue and it should be considered to be a neoplastic benign lesion.