The hull of the sunflower is a ligneous tissue that protects the embryo and cotyledons, and it is rich in wax esters (WEs). WEs are extracted from whole sunflower seeds together with the oil, conferring an undesirable turbidity on this product which must be removed through cooling and filtration for commercialisation. The analysis of sunflower oil WEs is hampered by the presence of significant amounts of sterol esters that co-elute with them in chromatography. Thus, we established here different methods based on GC/MS to analyse the WE content and composition of sunflower hulls, kernels and oil, and that of industrially crystallised sunflower WEs. Hence, using a combination of MS scanning and specific ion monitoring it was possible to quantify and characterise sunflower WEs, overcoming interference by other lipids in the sample. The results revealed that sunflower WEs were formed by saturated species from C40 to C60. The use of the new method for the analysis of WEs from species other than sunflower was also discussed.