Organochlorines such as PCBs, DDTs, HCHs, CHLs and HCB were determined in pooled whole body homogenized of fish samples collected from five locations during 1998 and 2003 in order to understand their contamination status, temporal and spatial variation in Indonesian waters. PCBs and DDTs were the predominant contaminants with concentrations from 9.7 to 2700 ng/g lipid wt. and 12 to 1100 ng/g lipid wt., respectively, while HCHs (nd-24 ng/g lipid wt.), CHL compounds (nd-81 ng/g lipid wt.) and HCB (0.22-28 ng/g lipid wt.) were one to two orders of magnitude lower. Among the locations, PCBs and CHLs were higher in the samples from highly industrialized and thickly populated-locations, whereas OC pesticides such as DDTs and HCHs were particularly more prominent in suburban and rural areas. Levels of OCs observed in the waters surrounding Java Island were higher than those in Sumatra Island, implying significant use of OCs in highly populated Java Island. Concentrations of PCBs and DDTs in fish from Jakarta Bay were significantly lower in the samples collected in 2003 as compared to fish in 1998, indicating decreasing trend of these compounds in the Indonesian environment. Recent estimated average daily intakes of PCBs (0.81 microg/person/day), DDTs (1.1 microg/person/day), HCHs (0.018 microg/person/day), CHLs (0.010 microg/person/day) were much lower than the threshold values recommended by various agencies, suggesting minimal risk of this compound via fish ingestion to Indonesians.