A new method based on comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC x GC-ToF MS) has been developed for the first time for the analysis of complex mixtures of disaccharides previously converted to their trimethylsilyl oximes (TMSO). Among the different experimental parameters considered for optimization, both the column set combination and the dimensions of the second-dimension column were found to be the most significant with regard to the complete resolution of structurally similar disaccharides. Application of the optimized method to honey analysis allowed the separation of most of the honey disaccharides previously described in the literature. Furthermore, 12 other unknown disaccharides have been separated by this method and characterized from their mass spectral data.