A new column association using comprehensive two-dimensional gas chromatography for the detailed molecular analysis of hydrocarbon mixtures is reported in this paper. In order to compare the impact of two different secondary columns, a novel column combination relying on a GC x 2GC system was used. This system is based on a non-polar first column (PONA) combined with both a permethylated beta-cyclodextrin (beta-Dex 120) stationary phase and a polysilphenylensiloxane (BPX 50) in the second dimension. Compared to BPX 50 stationary phase, the implementation of beta-cyclodextrin columns as the second dimension was found to improve the resolution between paraffins and naphthenes in the naphtha range but not in the middle distillate range. Attempts to improve the results and to understand the interaction mechanism remained unsuccessful. Therefore, the benefits of the beta-Dex 120-column are only demonstrated on heavy naphtha cut for the quantitation of hydrocarbons.