Concentrations of organochlorines such as PCBs, DDTs, chlordanes (CHLs), HCHs and HCB were determined in the liver of common cormorants from two different colonies to understand the current status of contamination and geographical differences. The birds from Shinobazu pond, central Tokyo, exhibited significantly higher OC levels than those in the Lake Biwa. Residue level of PCBs was the highest followed by the DDTs regardless of the locations and growth stages. CHLs and HCB were also higher in the Shinobazu pond adults and juveniles, whereas HCHs were comparable with the Lake Biwa. The OC levels, excluding PCBs, were relatively higher in regurgitated fish in Lake Biwa than Tokyo Bay fish. The inverse relation of bioaccumulation between fish and birds emphasized that cormorants from both colonies, at least, would have seasonal and preferential feeding habits in a widely extended area. The calculated biomagnification values showed that DDTs and CHLs had lowest and highest metabolic capacities, respectively. This study also made evident that present OC contamination levels in common cormorants may not pose a serious threat to their reproduction. However, contaminant related risk in cormorants, if any, could be higher in Shinobazu pond than that in Lake Biwa.