Two commercially important fish species, Nile perch (Lates niloticus) and Nile tilapia (Oreochromis niloticus) belonging to different trophic levels were collected from the Napoleon Gulf and Thurston Bay in Lake Victoria. Polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs) and dioxin-like polychlorinated biphenyls (dl-PCBs) were extracted from the fish muscles and livers using the (13)C isotope dilution method, followed by multiple column chromatography clean-up. Analysis was achieved by a high resolution gas chromatography coupled with a high resolution mass spectrometer. The concentrations of analytes ranged from 0.07 to 0.59pgg(-1) fresh weight (fw) and 0.3-19.0pgg(-1) in L. niloticus and 0.06-0.18 and 0.2-15.7pgg(-1) in O. niloticus, for ∑PCDD/Fs and ∑dl-PCBs, respectively. Differences in congener concentrations were observed between the two fish species and study sites, and this was attributed to differences in feeding habits and trophic levels. World Health Organization-toxic equivalents (WHO-TEQs) were in the range 0.01-0.16pgTEQg(-1) for the PCDD/Fs and 0.001-0.74pgTEQg(-1) for the dl-PCBs. The TEQ values in the present study were lower compared to those of most fish samples reported in literature and were within permissible levels recommended by the European Union, implying that the fish was fit for human consumption.