Polychlorinated dibenzo-p-dioxins and dibenzofurans, commonly called dioxins, have been compounds of concern for decades. Dioxins, along with polychlorinated biphenyls (PCBs) and polychlorinated naphthalenes (PCNs), are considered persistent organic pollutants or POPs. Dioxins, PCBs, and PCNs are halogenated aromatic compounds, and all three compounds pose similar toxicological concerns to animals. As the name POPs suggests, these compounds are known to be chemically stable in the environment and bioaccumulate in animals. There are numerous studies on the health effects of dioxins, PCBs, and PCNs in a variety of organisms. However, the low concentrations of these compounds found in the environment and their bio-accumulative effects raise concerns over chronic, rather than acute, health issues. The analysis of dioxins, PCBs, and PCNs is challenging due to their low concentration detection requirements, hundreds of possible congeners, and complicated sample matrix. Due to these challenges, the analysis of these compounds is generally performed by gas chromatography coupled to mass spectrometry (GC-MS). There are extensive studies published on the analysis of PCBs and dioxins on a variety of GC separation columns as well as studies on detection limits of the instrumentation used. However, there has been little focus on defining instrument performance, column selectivity, and identifying coelutions on various column phases, which is the goal of the following studies. Traditionally, dioxin analysis has been performed by gas chromatography coupled to a high-resolution mass spectrometer (GC-HRMS). GC-HRMS has historically provided the selectivity and sensitivity necessary to analyze dioxins; however, they are limited by the number of compounds they can monitor for at a time and are larger than newer benchtop models. Additionally, HRMS instruments are being phased out, due to issues with the metals used in the construction of the magnets. Benchtop mass spectrometers such as triple quadrupoles (MS/MS), quadrupole time of flight (Q-TOF), and TOF instruments are potentially capable of the same selectivity and sensitivity as the GC-HRMS system. These instruments offer advantages in the number of compounds that can be monitored for at a time and ease of use over the GC-HRMS. However, even with the advantages provided by these newer instruments, the GC-HRMS is still singled out as the instrument of choice in regulatory methods. A comparison was made between the GC-HRMS and five benchtop instruments with a method detection limit study to show that these newer instruments are capable of the same selectivity and sensitivity as the GC-HRMS system and can be used for regulatory dioxin analysis. Instrument sensitivity is an important factor in dioxin, PCB, and PCN analysis as these compounds are found at trace levels in the environment and animals. However, selectivity for these compounds is just as important a consideration as sensitivity. Dioxins have a possible 5020 unique congeners. That number includes the 210 chlorinated dioxins, 17 of which are considered toxic, 210 brominated dioxins, and 4600 mixed chlorinated/brominated compounds. PCBs have 209 chlorinated congeners, and PCNs have a possible 75 chlorinated congeners. Selecting the correct stationary phase is essential to characterize the toxicity of a sample accurately, as many of the congeners coelute. Nine popular GC columns were characterized for their ability to separate dioxins, PCBs, and PCNs using a retention index system. The retention index values for two columns were plotted against each other to obtain a selectivity graph. These graphs can be used to identify which columns provide the most significant selectivity difference for the compounds of interest. The retention indices generated also serve as a secondary means of analyte identification. These graphs were then used to identify a unique confirmation column pair for use with UESPA method 1613. The Rxi-17SilMS and Rtx-Dioxin2 columns showed unique selectivity for dioxins that can be used to fulfill the requirements of the USEPA-1613 method. Finally, this column combination is used with comprehensive 2-dimensional chromatography to develop a single analytical method to separate the toxic dioxin congeners from other dioxins and interfering compounds. The following research presented in chapters 2-6 has all been submitted for peer-reviewed publication. Chapter 2 has been published in the Journal of Mass Spectrometry. Chapter 3 has been published in the Journal of Chromatography A. Chapters 4, 5, and 6 are currently under peer review for publication in the Journal of Chromatography A. I directly contributed to all the research presented in this dissertation and am listed as the first author on all publications.