The interacting roles of food web structure and lipid content on bioaccumulation of PCB and DDT in lake trout (Salvelinus namaycush) was evaluated in Ontario inland lakes and Great Lakes. It previously has been reported that longer food chains resulted in greater bioaccumulation of PCBs (Rasmussen et al. 1990. Can. J. Fish. Aquat. Sci. 47: 2030-2038); however, longer food chains also resulted in increased lipid content, and it is uncertain whether the measured bioaccumulation was attributable to food chain length or Lipid content. ANCOVA demonstrated that both factors are significant. PCB and DDT concentrations were each proportional to lipid content in all systems but the magnitude of the concentrations varied, due to either food chain length or differences in contaminant loading. It is suggested that the presence of Mysis relicta is especially important with respect to the observed food web effects and as a vector for contaminant transport from contaminated sediments. Significant differences between the Great Lakes and inland lakes were identified which largely result from differences in loadings of contaminants. The observed significant relationship between concentrations of PCBs and DDTs suggests that similar relationships could apply to other contaminants with similar chemical and bioaccumulative properties.