As part of a project funded by the Massachusetts Bay Program, soft-shell clams were collected from 5 polluted sites around Boston Harbor that contained variable amounts of pollutants (including PCBs and PAHs), and 2 relatively non-polluted sites (controls) in Cape Cod Bay. Animals were bled, measured, fixed in Trumps, and processed in paraffin. Several histopathologic parameters were identified and evaluated in 20 animals from each site. Histologic lesions highly correlated with animals sampled from polluted sites were kidney epithelial hyperplasia, kidney brown cell accumulation, gonadal inflammation, parasites of the kidney and connective tissues, pericardial gland hypertrophy, gill inflammation, and gill papillomas. Neither of the two tumor types identified (including leukemia) appeared to be correlated with animals sampled from polluted areas. These findings showed that while the evaluation of only one lesion type cannot be used to determine the effects of pollution on soft shell clams, a cumulative lesion index may provide a significant relative method of evaluating pollution effects.