Comprehensive two-dimensional gas chromatography (GC×GC) was used in this work in order to reveal and identify minor compounds of several raw materials in biodiesel samples, which are not detected by conventional GC analysis. Multiway principal component analysis (MPCA) of the chromatographic profile allowed to identify compounds as C15:1n-3, C18:2n-6, C20:1n-6, C20:3n-3, C20:3n-6, C20:4n-6 C20:5n-3, C21:1n-6, C22:1n-9, C23:1n-9, C24:1n-9 multiunsaturated which were useful tracers to discriminate between biodiesel samples. In this way, the separation power of GC×GC combined with the MPCA algorithm proved to be a valuable strategy for biodiesel samples classification, allowing identification and providing additional compounds of the commonly known as chemical profile of biodiesel samples.