Relationships between hepatic lesions and chemical contaminant concentrations in sediments, stomach contents, and tissues were examined in winter flounder (Pleuronectes americanus) collected from 22 sites in eight major embayments on the Northeast Coast (i.e., Salem Harbor, Boston Harbor, Plymouth Bay, Buzzards Bay, New Bedford Harbor, Narragansett Bay, Long Island Sound, and Raritan Bay). Prevalences of a number of pathological conditions, including neoplasms, preneoplastic lesions, hydropic vacuolation, and other necrotic and proliferative lesions, were significantly elevated in fish from contaminated urban embayments such as Boston Harbor and Raritan Bay. Results of logistic regression analyses indicated that polycyclic aromatic hydrocarbons, DDTs, or chlordanes in sediments, stomach contents, liver, or bile of winter flounder were significant risk factors for the development of several lesion types, including hydropic vacuolation and proliferative and necrotic lesions. However, concentrations of PCBs in sediments and tissue were not significant risk factors for any of the lesions observed. In addition to chemical contaminants, fish age and sampling season had a significant influence on disease occurrence. The risk of hepatic disease increased with age, and lesion prevalences were higher in animals collected during the spring than in winter when spawning migration was taking place. The relationships observed in this study strongly suggest an association between exposure to certain chemical contaminants and the development of particular liver lesions in winter flounder.