Standard solutions containing a mixture of seven sterols and 5α-cholestane as internal standard, and sample mixtures that comprised varying ratios of sterol and stanols from green lip mussel tissue and dried cow faeces were analysed by using comprehensive two-dimensional gas chromatography (GC×GC). Quantitative results were compared with single-column GC analysis. The latter samples included sterols of interest, but which cannot be readily obtained elsewhere. It may also mimic potential environmental samples where dairy production and aquaculture (oyster, mussel cultivation) share the same catchment; environmental sterol signatures may exhibit characteristics of both sample types comprising this mixture. Whereas single-column GC-flame ionisation detection was unable to reliably quantitate target sterols, the GC×GC experiment permitted small amounts of sterols and stanols to be detected and separated. Likewise GC-MS analysis was unable to detect some of the minor sterols which coeluted on a single column. The GC×GC mode allows complete separation of several important sterols and stanols, such as 24-ethylcoprostanol, campesterol and 24-methylenecholesterol, demonstrating the enhanced resolving power of the GC×GC system. Separation of 24-ethyl-epi-coprostanol from several algal-derived interfering components was achieved, leading to higher degree of confidence in the quantitative analysis of faecal sterols. The effects of a number of operating variables - column length, carrier flow-rate and elution temperature - on component resolution and presentation of data in the two-column analysis are described.