Most lipids are a complex mixture of classes of compounds such as fatty acids, fatty alcohols, diols, sterols and hydroxy acids. In this study, the suitability of comprehensive two-dimensional gas chromatography coupled to a time-of-light mass spectrometer is studied for lipid characterization in complex samples. With lanolin, a refined wool wax, as test sample, it is demonstrated that combined methylation plus silylation is the preferred derivatization procedure to achieve (i) high-quality GC x GC separation and (ii) easily recognizable ordered structures in lipid analysis. Optimization of the GC x GC column combination, the influence of the temperature programme on the quality of the separation, and the potential and limitations of automated TOF-MS-based identification are discussed. The combined power of a 2D separation, ordered structures and MS detection is illustrated by the identification of several minor sample constituents.