Contaminant effects on defence responses of ecologically and economically important organisms, such as the Pacific oyster Crassostrea gigas, are likely to influence their ability to resist infectious diseases, particularly at the young stages. The aim of this study was to explore the potential relationships between organic contaminants accumulated in the soft tissues of juvenile oysters, defence responses and physiological condition. Oysters were transplanted during summer and winter periods in different sites in the Marennes-Oléron Bay, the first area of oyster production in France, and in the Gironde Estuary, the biggest estuary in Occidental Europe. Among the battery of biochemical and physiological biomarkers applied in the present work (superoxide dismutase -SOD-, catalase, glutathione peroxidase -GPx-, malondyaldehyde -MDA-, catecholase, laccase and lysozyme in gills, digestive gland, mantle and haemolymph, glycogen, proteins and lipids in the digestive gland and the condition index at the whole organism level), MDA and lysozyme in the digestive gland and SOD, GPx and laccase in plasma contibuted to significantly discriminate sites in which oysters bioaccumulated different levels of heavy polycyclic aromatic hydrocarbons (HPAHs), polychlorobiphenyls (PCBs), polybromodiphenylethers (PBDEs), dichlorodiphenyltrichloroethanes (DDTs) and lindane. These results strengthen the hypothesis that it is possible to differentiate sites depending on their contamination levels and biological effects by carrying out studies with transplanted juvenile oysters. In addition, correlations between antioxidant and immune defence responses and PAH and DDT body burdens in the first area of oyster production in France, the Marennes-Oléron Bay, and where massive oyster mortalities have been reported, suggest that the presence of organic chemical contaminants in the Marennes-Oléron Bay may influence defence responses in juveniles of C. gigas, and, therefore, could influence their ability to resist infectious diseases.