In order to assess the biological effects of the Prestige oil spill (POS), mussels (Mytilus galloprovincialis), European hake (Merluccius merluccius) and European anchovy (Engraulis encrasicolus) were sampled between April and September 2003 in various geographical areas of Bay of Biscay: Galicia, Central Cantabrian and East Cantabrian. In mussels, several cell and tissue biomarkers were measured: peroxisome proliferation as induction of acyl-CoA oxidase (AOX) activity, lysosomal responses as changes in the structure (lysosomal volume density, V(V(L)), surface-to-volume ratio, S/V(L), and numerical density, N(V(L))) and in membrane stability (labilization period, LP), cell type replacement as relative proportion of basophilic cells (volume density of basophilic cells, V(V(BAS))) in digestive gland epithelium, and changes in the morphology of digestive alveoli as mean luminal radius to mean epithelial thickness (MLR/MET). Additionally, flesh condition index (FCI) and gonad index (GI) were measured as supporting parameters. In hake and anchovy, liver histopathology was examined to determine the prevalence of parasites, melanomacrophage centers, non-specific lesions (inflammatory changes, atrophy, necrosis, apoptosis), early non-neoplastic toxicopathic lesions (i.e., hepatocellular nuclear polymorphism), foci of cellular alteration, benign and malignant neoplasms. In mussels, AOX induction was noticeable in April except in Galicia. LP values were low in all the geographical areas studied, indicating disturbed health, especially in Galicia. Alike, lysosomal enlargement was observed in most stations as shown by the extremely low S/V(L) values. V(V(BAS)) and MLR/MET values were markedly high. Overall, employed biomarkers detected exposure to toxic chemicals and disturbed health in mussels from Bay of Biscay, with impact decreasing from April to September. Although hepatocellular nuclear polymorphism and nematode parasitization in fish liver were remarkably prominent in some areas, they cannot be hitherto related to POS, since we lack historical data to determine whether the prevalences found were normal or significantly raised after POS.