Chlorinated paraffins (CPs) are emerging persistent organic pollutants that has been produced for a several decades, but information on their environmental fate are lacking. CPs are divided into three classes (short-chain, medium-chain and long-chain) and CP mixtures can comprise thousands of isomers which provides a major analytical challenge. In this study, parameters on gas chromatograph coupled to a time-of-flight mass spectrometer (GC-qTOF-MS) in negative chemical ionisation mode were optimized which can improve the analysis of short-chain chlorinated paraffins (SCCPs). Comparison was made between GC-qTOF-MS and GC coupled to low resolution mass spectrometer (LRMS) in electron capture negative ionisation mode. Two quantification procedures were applied on analysed standards and technical mixtures to compare and determine the advantages and disadvantages of each procedure. The deconvolution procedure applies a mathematical algorithm to the sample in order to deconvolute the CP congener group pattern and provides quantification of the total SCCP content. The response factor procedure compensates for differences in response factors between different CP mixtures and provides CP congener pattern and amount of SCCP in the sample. The high resolution GC-qTOF-MS provided a higher sensitivity when it comes to quantifying SCCPs and differentiating SCCPs from interferences. An ion source and quadrupole temperature at 150 ºC and 110 ºC, respectively, along with an emission at 6 μA and an electron energy at 250 eV gave the highest intensity among the tested parameters. Both quantification procedures show promise with the deconvolution procedure having an advantage by the possibility of being able to view the contribution from different standards. Interferences constitutes a major problem but can be avoided by use of HRMS and careful integration of chromatograms.