A novel cryogenic modulator was constructed for comprehensive two-dimensional gas chromatography (GC x GC). The modulator is based on two-step cryogenic trapping with CO2 and thermal desorption with electric heating. The GC x GC system included a nonpolar first-dimension column and two semipolar second-dimension columns, one connected to a flame ionization detector and the other one to a electron capture detector. A Matlab-based program, which allowed determination of peak heights and volumes, was written for the data analysis. The GC x GC system was applied for the analysis of polyaromatic hydrocarbons and polychlorinated biphenyls. The functioning of the modulator and the quantitativity of the method were studied with both peak volumes and peak heights from a three-dimensional plot. The separate peak areas from the modulated chromatogram were calculated as a comparison. The quantitative results were compared with those obtained with the same system but without the thermal modulation. The method was found to be repeatable and linear with use of peak volumes as well as peak heights. There was also good agreement with the results obtained by integration of separate peak areas. The developed GC x GC method was applied to the analysis of a Soxhlet extract of a certified sediment sample. The results were compared with the certified values.