The analysis of polychlorinated dibenzofurans (PCDFs), dibenzo-p-dioxins (PCDDs) and to some extent biphenylenes (PCBPs) by high-resolution gas chromatography (HRGC) and mass spectrometry is described. Electron-impact (EI) and negative chemical ionization (NCI) mass spectrometry were used, and their application in environmental analyses documented. NCI shows increased sensitivity to all PCDFs and PCDDs except for 2,3,7,8- and other tetra-CDD isomers. The identification of the various PCDFs and PCDDs, specifically the identification of the toxic and hazardous 2,3,7,8-substituted isomers is emphasized; the unambiguous identification of all 2,3,7,8,-substituted PCDDs is documented. The application of HRGC and mass spectrometry to isomer-specific analyses of samples of aquatic species from the Baltic and the Great Lakes is shown. Results from this and previous studies indicate PCDF and PCDD residues in these organisms including significant levels of 2,3,7,8-substituted isomers. These aquatic species apparently show preferential retention or reduced metabolization rates for these toxic isomers. The results of samples from the Baltic indicate a contamination primarily due to PCDFs. The origin of this contamination seems complex and related to PCBs as well as chlorophenols. PCDF and PCDD isomer distribution patterns from analyses using HRGC and mass spectrometry aid in the identification of origin, sources and elucidation of routes of formation of these compounds. These methods are indispensable in taking measures to reduce future contaminations and to protect our environment.