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There are six Areas of Concern, as identified by the International Joint Commission, located in New York State. Three are contiguous in western New York and have similar contaminants (Buffalo River, Niagara River, and 18 Mile Creek). We used the Statewide Planning and Research Cooperative System database, which records diagnoses according to the International Classification of Disease, Ninth Revision codes for all patients admitted to state-regulated hospital facilities, to compare incidence of selected diseases reported in hospitalized patients who reside in ZIP codes that are within 15 miles of any of these sites to those of residents of three different control populations: all residents of the rest of New York State (including New York City), all residents of ZIP codes outside New York City that do not contain any site identified as a federal or state Superfund site, and all residents of ZIP codes outside New York City that contain a federal or state Superfund site that does not have one or more persistent organic pollutants listed as a major contaminant. We found a significant elevation of disorders of the thyroid gland in women, but not in men, of all ages greater than 25 years on all three comparisons, as well as an increased incidence of morbidity from diseases of the female genital tract in women between age 25 to greater than 75 years for all comparison groups. There was also a significant elevation in incidence of endometriosis in women 25–44 years of age. All these elevations were significant at the 99% confidence level. Incidence of diseases of ovaries and testes and female infertility were not different from those in the rest of New York State. Although many factors influence incidence of thyroid and genital diseases, our results are consistent with the hypothesis that exposure to environmental contaminants through residence near polluted sites may be a factor. Key words: endometriosis, genital disease, hospitalization, ovaries, testes, ... [ABSTRACT FROM AUTHOR]