A clean-up method for polybrominated dibenzo-p-dioxins (PBDDs), dibenzofurans (PBDFs) and diphenyl ethers (PBDEs) was modified using combinations of multi-layered silica gel, Florisil and active carbon columns. By using active carbon column chromatography in the final procedure, PBDEs were well separated from PBDD/Fs in an elution test with reference standards. We report the application of this method to sediment samples taken from industrialized areas in Japan. These sediments contained PBDEs ranging in concentration from 13 to 2394 pg/g, dry wt. PBDEs did not interfere with the quantification of PBDD/Fs. In addition, PBDEs found in the PBDD/F fraction did not interfere with the identification of PBDFs using the HRGC/HRMS separation method. Some 2,3,7,8-tetra- to hexabrominated dioxins and furans were also detected in the sediment samples.