In the current energetic context (increasing consumption of vehicle fuels, greenhouse gas emission etc.) government policies lead to mandatory introduction in fossil fuels of fuels resulting from renewable sources of energy such as biomass. Blending of fatty acid alkyl esters from vegetable oils (also known as biodiesel) with conventional diesel fuel is one of the solutions technologically available; B5 blends (up to 5%w/w esters in fossil fuel) are marketed over Europe. Therefore, for quality control as well as for forensic reasons, it is of major importance to monitor the biodiesel origin (i.e. the fatty acid ester distribution) and its content when it is blend with petroleum diesel. This paper reports a comprehensive two-dimensional gas chromatography (GC x GC) method that was developed for the individual quantitation of fatty acid esters in middle distillates matrices. Several first and the second dimension columns have been investigated and their performances to achieve (i) a group type separation of hydrocarbons and (ii) individual identification and quantitation of fatty acid ester blend with diesel are reported and discussed. Finally, comparison of quantitative GC x GC results with reference methods demonstrates the benefits of GC x GC approach which enables fast and reliable individual quantitation of fatty acid esters in one single run. Results show that under developed chromatographic conditions, quantitative group type analysis of hydrocarbons is also possible, meaning that simultaneous quantification of hydrocarbons and fatty acid esters can be achieved in one single run.