Comprehensive two-dimensional gas chromatography–mass spectrometry (GC × GC–MS) has beenshown to permit for the unprecedented chromatographic resolution of volatile analytes encompassingvarious families of organic compounds. However, peak identification based on retention time, two-dimensional mapping, and mass spectrometric fragmentation only, is not a straightforward task yet.The possibility to establish molecular links between constituents is of crucial importance to under-stand the overall chemistry of any sample, especially in natural extracts where biogenetically relatedisomeric structures are often abundant. We here present a new way of using GC × GC that allows search-ing for those molecular connectivities. Analytical investigations of essential oil constituents by meansof GC × GC–MS permitted to observe in real time the thermally-induced transformations of varioussesquiterpenic derivatives. These transformations generated a series of well-defined two-dimensionalpeak bridges within the 2D-chromatograms connecting parent and daughter molecules, thus permittingto build a clear scheme of structural relationship between the different constituents. GC × GC–MS appearshere as a tool for investigating chromatographic phenomena and analyte transformations that could notbe understood with conventional GC–MS only.