Winter flounder, Pseudopleuronectes americanus, from Boston Harbor near the Deer Island sewage outfall and from a nearby reference population near Plymouth Beach, Massachusetts, USA, were collected on several occasions and analysed for a variety of biochemical variables and histopathological conditions. A number of biochemical variables including hepatic and pectoral fin ascorbic acid concentrations, hepatic glycogen and lipid levels, plasma glucose concentrations, brain serotonin and norepinephrine concentrations, and the concentration and ratio of various free amino acids in muscle tissue were significantly different between the two populations. The apparent apoptotic hepatic lesions were found in the majority of the winter flounder collected from Boston Harbor and were rarely observed in animals from the reference site. Low tissue concentrations of ascorbic acid and hepatic glycogen were found to have significant statistical associations with the presence and degree of severity of these hepatic lesions.