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Chromosomal and genomic instability due to telomere dysfunction plays an important role in carcinogenesis. To study telomere shortening in the oesophageal epithelium of alcoholics, we measured the telomere lengths of basal and parabasal cells in comparison with those of non\u2010alcoholics using Q\u2010FISH and our original software, Tissue Telo, and also assessed histological inflammation. Telomeres in basal cells were significantly shorter in alcoholics than in age\u2010matched normal controls. Prominent histological findings of chronic inflammation were not evident in either alcoholics or non\u2010alcoholics. Our finding that telomeres in the oesophageal epithelium are shorter in alcoholics than in non\u2010alcoholics indicates that telomere shortening may be associated with the frequent occurrence of squamous cell carcinoma in alcoholics. Further studies to clarify the reason for the large annual loss of telomere length with rapid turnover or lower telomerase activity in the oesophageal epithelium of alcoholics will be necessary. Copyright \u00a9 2010 Pathological Society of Great Britain and Ireland. 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