In recent years, food authentication, in terms of geographical and varietal/animal origins, is considered of primary importance at all levels of the production process. Therefore, it is clear that there is an economic basis to develop analytical methods able to certify the declared origin of food products, in order to protect consumers and honest producers from fraud and unfair competition, respectively; consequently, during recent years, several food authentication techniques have been proposed. This review attempted to present in a critical way the contribution of High Resolution Nuclear Magnetic Resonance (HR-NMR) and Isotope Ratio Mass Spectrometry (IRMS) techniques in the assessment of quality and authenticity, mainly in terms of characterization of geographical and varietal origin, of wheat and wheat products, focusing on the most important studies to this direction.