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Seven biomarkers in 204 spottail shiners Notropis hudsonius were examined for effects of pollution and parasites on fish health at localities along the St Lawrence River, Canada. The number of pigmented macrophage centres and pigmented macrophages in the spleen was significantly higher at polluted localities receiving urban and industrial effluents than at reference localities, indicating that they were good indicators of exposure to pollution in spottail shiners. Seven of the nine species of parasites found in 1+ year fish showed significant correlations with biomarkers. More parasites (18 species) but fewer correlations with biomarkers were observed in 2+ year fish, indicating that parasite effects were more pronounced in young spottail shiners. A significant negative relationship was observed between condition factor and Neoechinorhynchus rutili in 1+ year fish, suggesting its potential pathological significance in young spottail shiners. High abundance of Plagioporus sinitsini was associated with higher spleen macrophage counts and lower indices of condition at polluted localities. Furthermore, infection by P. sinitsini in polluted conditions appeared to have a greater negative effect on fish health than either stressor alone, providing further evidence that parasites should be considered when examining effects of pollution on fish health.