Polychlorinated dibenzo-p-dioxins and furans are environmentally persistent and highly toxic compounds. 136 chlorinated dioxins and furan congeners contain at least four chlorine atoms and pose a complex separation challenge in environmental and biological matrixes. The complexity arises from the dioxin and furan molecules with substitutions at positions 2, 3, 7, and 8, which are toxicologically relevant but are not easily separated from the other non-/less toxic congeners. Many regulatory methods require the use of two columns with different polarities or selectivity for dioxin analysis. The most common confirmation column pair is a (5% phenyl)-methylpolysiloxane and a (biscyanopropyl-/ cyanopropylphenyl)-methylpolysiloxane. These phases are required in USEPA-1613 for 2,3,7,8-tetrachlorodibenzo-p-dioxin and 2,3,7,8-tetrachlorodibenzofuran specificity. However, other column phases, such as the Rxi-17SilMS and the Rtx-Dioxin2, offer alternatives to the traditional column pairing and provide a similar or better separation of 2,3,7,8-substituted congeners. This study compares four columns for dioxin analysis: the Rtx-Dioxin2, Rxi-17SilMS, Rxi-5SilMS, and Rtx-2330. All columns used in this study are capable of meeting the requirements for dioxin analysis required by USEPA-1613. However, the Rtx-Dioxin2 demonstrated improved selectivity for a wider range of dioxin compounds than the Rxi-5SilMS. The Rtx-Dioxin2 is capable of resolving 2,3,7,8-tetrachlorodibenzo-p-dioxin and 2,3,7,8-tetrachlorodibenzofuran from common interferants better than the Rxi-5SilMS and can be used as a confirmation column with either the Rtx-2330 or Rxi-17SilMS.