Abstract An Estonian pyrolysis shale oil has been characterized using comprehensive two dimensional gas chromatography (GC × GC) coupled to a flame ionization detector (FID) and time of flight mass spectrometer (TOF-MS). Oxygen containing compounds were abundant and the following classes were identified: benzenediols, hydroxybenzofurans, phenols, ketones, and naphthols. The large peak overlap observed for oxygenates with the hydrocarbon matrix using a non-polar × polar column combination made identification and quantification difficult. A methodology based on the more selective separation using a polar × non-polar and polar × mid-polar column configurations was developed and tested. The obtained bidimensional resolution confirms that the method provides an improved separation of unsaturated hydrocarbons, mid-polar and even highly polar oxygen containing compounds. The use of an internal standard methodology allowed complete quantification of the pyrolysis shale oil both by carbon number and chemical class.