A method for trace analysis of polybrominated diphenyl ethers (PBDE) in fish based on gas chromatography/electron ionization high resolution mass spectrometry (GC/EI-HRMS) was developed, and levels of PBDE were determined in whitefish (Coregonus sp.) from eight Swiss lakes and in rainbow trout (Oncorhynchus mykiss) from four Swiss fish farms. PBDE concentrations (sum of PBDE congeners BDE-28, BDE-47, BDE-99, BDE-100, BDE-153, BDE-154, and BDE-183) in filet from whitefish between 36 and 165 ng/g lipid weight (lw) were found, corresponding to wet weight (ww) concentrations of 1.6-7.4 ng/gww. PBDE contents in filet from farmed rainbow trout were significantly lower than in wild whitefish (12-24 ng/glw, 0.74-1.3 ng/gww), and the PBDE congener patterns were different for both species (a higher BDE-47 to BDE-99 ratio for farmed rainbow trout compared to wild whitefish was found). Whitefish PBDE levels [ng/glw] correlate better with the surface/volume ratio of the respective lakes (r(2)=0.70) than with other lake properties such as catchment area (size or number of inhabitants) or residence time, suggesting atmospheric deposition as an input pathway for PBDE. Based on an average daily consumption of 20 g whitefish (Switzerland) with a PBDE content of 7.4 ng/gww (highest PBDE concentration detected in this study), a maximum daily intake of 0.15 microg PBDE was estimated (0.026 microg/day for farmed trout). This number corresponds to the lower end of the estimate for the total PBDE intake of the Nordic consumer of 0.2-0.7 microg/day.