The suitability of four mass spectrometric methods for the gas chromatographic analysis of polychlorinated n-alkanes (PCAs, also called chlorinated paraffins) was evaluated and compared using spiked and fish liver samples. Electron ionization tandem mass spectrometry (EI-MS/MS) as well as electron capture negative ionization (ECNI) combined with low and high resolution mass spectrometry and CH4/CH2Cl2-negative ion chemical ionization (NICI) low resolution mass spectrometry were investigated. All methods showed an accuracy of <21% for the analysis of spiked fish samples. However, the analysis of real samples showed deviations of up to 46% between the four mass spectrometric methods. The influence of the selected reference standard on quantification was also evaluated. The use of a quantification standard with a degree of chlorination deviating from that of the sample can result in differences of > 100% for the ECNI methods. EI-MS/MS and CH4/CH2Cl2-NICI led to errors of maximum 17% and 33%, respectively, independent from the degree of chlorination of the used reference standard.