The volatile headspace from two coffee bean varieties, namely Arabica (Coffea arabica) and Robusta (Coffea canephora ex Froehner), were sampled by using solid-phase microextraction (SPME), and then analysed with comprehensive two-dimensional gas chromatography interfaced to a time-of-flight mass spectrometer (GC x GC-TOFMS). Two distinct column set combinations were investigated--an apolar-polar and polar-apolar configuration--and the separation achieved from each set was compared. Results were compared with a previous literature report for coffee analysed by GC x GC-FID, using an analogous polar-apolar column set combination, where authentic standards were used to confirm the position of the selected components in the 2D separation space. The present study provides independent mass spectral confirmation of component identity, and demonstrates that the relative, structured position of these components is comparable in the two experiments. Total ion current (TIC) chromatograms were processed using ChromaTOF automated data processing software. It was necessary to restrict the number of processed peaks to 1000 (S/N > 100), which required approximately 8 h for processing. Extracted ion chromatograms were generated using prominent fragment ions, and unique masses, to aid in analyte identification process, and was particularly useful in instances of component peak overlap, and for the identification of pyrazine analytes (e.g. 44, 88, 122 u). Semi-quantitative analysis was restricted to the 44 selcted components; however, the omission of peaks with S/N < 100, limiting the processed peaks to 1000, reduced the semi-quantitative application of the GC x GC-TOFMS method developed. Finally, results gained from GC x GC-TOFMS and GC x GC-qMS analyses were comparable with respect to spectral similarity assignments for the 44 target analytes.