Most analytical methods for persistent organic pollutants (POPs) focus on individual groups of targeted analytes. Therefore, analysis of multiple classes of POPs typically entails several sample preparations, fractionations, and injections, whereas other chemicals of possible interest are neglected or lost. To analyze a wider scope of organic contaminants in fish oil, we developed an approach to combine the analysis of targeted and untargeted chemicals using an automated direct sample introduction (DSI) and comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry (GC x GC/ ToF-MS). DSI-GC x GC/ToF-MS is a powerful tool that attains high quality separations to achieve high selectivity while still providing a wide analytical scope with minimal sample preparation, especially in conjunction with DSr's high tolerance to dirty extracts. Gel permeation chromatography (GPC) was used for initial separation of lipids from POPs and other GC-amenable organic compounds from dietary cod liver oil. For comparison purposes, additional cleanup of the GPC extracts was done by silica adsorption and acidification, which helped provide clues in the identification of untargeted compounds, but in routine analysis, only GPC is needed for this analytical approach. The approach allowed simultaneous identification of known-POPs in the fish liver oils, and further permitted presumptive identifications of multiple groups of halogenated natural products (HNPs) and other organic chemicals of interest through comparisons of the mass spectra from analyses with those from mass spectral libraries and/or reports in the literature (approximately 60 PCB congeners and 76 compounds in total). Subsequent confirmations were made by reanalysis and comparison of chromatographic retention times and mass spectra with contemporaneously analyzed reference standards. Otherwise, ion fragmentation patterns of unknown compounds were assessed for tentative identifications. Some of the HNPs in the fish oils were detected and identified for the first time. Our study demonstrates that the wide monitoring scope provided by the DSI-GC x GC/ToF-MS method after GPC provides many logistical and performance advantages over the conventional use of several different methods designed for individual classes of targeted analytes after extensive sample preparation.