We examined perfluoroalkyl compounds (PFC) in bighead (BHCP; Hypophthalmichthys nobilis) and silver (SVCP; H. molitrix) carp from the Illinois River, Illinois, USA. Summed PFC concentrations in whole fish did not differ by species or river reach. Perfluorooctanesulfonate (PFOS) concentrations were much greater in whole fish (16.4 ng/g) than in fillets (3.4 ng/g). PFOS concentrations represented 35%-51% of total measured PFC concentrations in whole fish, and in fillets were weakly associated with carcass mass (R2=0.17, p=0.01) and % carcass lipid (R2=0.16, p=0.01). No such relationship was observed in whole fish. The relationship between concentrations of individual PFC congeners in whole fish and carcass mass or % lipid content varied by species. Our study demonstrated that filter-feeders such as BHCP and SVCP can accumulate measureable concentrations of PFC and these results are important for understanding the fate of these compounds in large river systems.