Chlorinated paraffins (CPs) are straight chain hydrocarbons that are produced as complex mixtures and are used as flame retardants and paint additives. These mixtures are extremely difficult to characterize using conventional chromatographic methods, as conventional gas chromatography results in unresolved complex chromatograms that preclude the identification and quantification of individual congeners or any reasonable assessment of the average carbon chain length. Carbon chain length is an important parameter for assessing physical properties and the toxicity of these materials. We have modified and improved a previously published gas chromatography-flame ionization detector method that uses Pd catalyst held in the gas chromatograph injector to simultaneously dechlorinate the CPs and separate the resulting alkanes. In addition, we have adapted this method to gas chromatography-mass spectrometry. Dehalogenation of other compounds was also studied with this system to investigate potential application to other complex halogenated mixtures.