Trematomus bernacchii sampled from two sites at Ross Island, Antarctica, were assessed for condition (gonadal and hepatic somatic indices and condition factor), pathological state (liver and gill histology), hepatic metal (Zn, Cu, Cd and Ni) concentrations, and metallothionein induction by quantitative competitive (qc) RT-PCR. Fish from a polluted site (Winter Quarters Bay) had pathological anomalies including necrosis and periductal inflammation in their livers, and X-cell disease, epithelial hyperplasia, lamellar fusion and aneurysms in their gills. Such anomalies were less common in fish from a relatively pristine site (Backdoor Bay, Cape Royds). Fish from both sites had similar liver concentrations of Zn, Cu and Cd and qcRT-PCR revealed similar levels of hepatic metallothionein mRNA. Ni in the livers of fish from Winter Quarters Bay were higher than those in fish from Backdoor Bay, but the differences were not great enough to affect hepatic metallothionein mRNA significantly. Despite the polluted state of Winter Quarters Bay waters, it seems that the heavy metals present may have only limited impact on the health status of fish collected from this locality. This may reflect a low bioavailability of the heavy metals in Ross Island marine sediments and suggests that other factors, such as relatively high levels of organic pollutants (PAHs, PCBs) or pathogens from the nearby sewage outlet, may play a more significant role in the aetiology of pathological conditions in fish from Winter Quarters Bay. 2000 The Fisheries Society of the British Isles