Cell and tissue pathology of both gill and digestive tissue has been the object of many research studies for the elucidation of contaminant-induced biological effects. In the present study, cellular pathological alterations were linked to subcellular sites of chemical accumulation in gills and digestive gland tissues. For this purpose, mussels (Mytilus edulis) were exposed to the organic contaminants aroclor 1254 (PCB), phenanthrene (PAH) or the metal lead (Pb). The localization of chemicals at the subcellular level was analysed by an antibody-based detection system and pathological changes were analysed in parallel in the same samples by transmission electron microscopy. After exposure to the different contaminants, cell organelles such as mitochondria and the endo-lysosomal system showed clear evidence of chemical-induced alterations. Large numbers of crystalloid inclusions were found in mitochondria and lysosomes after organic contaminant exposure. Immunocytochemical detection of the chemicals showed their accumulation inside of various cell organelles such as lysosomes, mitochondria, and nuclei. Additionally, chemicals were localized in association to membranes, cilia and microvilli of gill and digestive gland cells. Furthermore, the chitinous rod and mucous secretions of gill epithelia cells were positively labelled for contaminants. Localization of contaminants by immuno-detection in combination with pathological diagnosis gives insights into the cellular targets of chemical attack.