Polybrominated diphenyl ethers (PBDEs) were analyzed in 88 forage fish samples collected from Lake Michigan in 1995 and in 2002/2003. Lipid-normalized total PBDE concentrations ranged from 149 to 1094 ng/g. Total PBDEs in alewife and deepwater sculpin did not change significantly from 1995 to 2002/2003, while the levels in bloater chub and the slimy sculpin decreased. BDE-47 was the most abundant congener in the fish. All of the forage fish were depleted in BDE-99 relative to what would be expected based on the congener composition of the commercial formulation in use. The deepwater sculpins were particularly lacking in BDE-99. Changes in the food web brought about by the dramatic decline of Diporeia abundance (due to the invasion of zebra and quagga mussels) may have affected the levels of PBDEs in some of the forage fish.