The sterlet (Acipenser ruthenus L.) is a bottom-feeding fish species with a direct exposure to contaminants from water and sediments. Although heavy metal pollution is believed to be one of the main threats to the sterlet population in the Danube River basin, there is a lack of knowledge of the exact impact of heavy metals on their survival. In the present study, effects of heavy metal pollution on sterlet in the Danube basin were assessed as well as the utility of different sterlet organs and tissues as indicators of heavy metal contamination. The sterlet were sampled at three different sites in the Danube basin, in Hungary and Serbia, isolated from each other by dams. Heavy metal analysis included measurement of Cd, As, Pb, Cr, Hg, Cu, Ni, Fe, Mn, and Zn concentrations in sterlet gills, muscle, liver, and intestine, and histopathological analyses comprised assessment and scoring of the extent and intensity of alterations in skin, gills, and liver tissue. Analysis revealed a significant presence of sublethal histopathological changes that were most pronounced in the liver and skin and increased accumulation of heavy metals, with the highest concentrations in the liver. Canonical discriminant analysis showed significant differentiation among the three studied localities, suggesting that the heavy metal concentrations in sterlet populations were site specific. The present study concludes that the accumulation of heavy metals is a response to the presence of these pollutants in the environment, and, together with other pollutants, it affects the vital organs of natural sterlet populations. Environ. Toxicol. Chem. 2010;29:515–521. © 2009 SETAC