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The nutritional value of breadmaking cereal spelt (Triticum aestivum ssp. spelta) is said to be higher than that of common wheat (Triticum aestivum ssp. vulgare), but this traditional view is not substantiated by scientific evidence. In an attempt to clarify this issue, wholemeal and milling fractions (sieved flour, fine bran, and coarse bran) from nine dehulled spelt and five soft winter wheat samples were compared with regard to their lipid, fatty acid, and mineral contents. In addition, tocopherol (a biochemical marker of germ) was measured in all wholemeals, whereas phytic acid and phosphorus levels were determined in fine bran and coarse bran samples after 1 month of storage. Results showed that, on average, spelt wholemeals and milling fractions were higher in lipids and unsaturated fatty acids as compared to wheat, whereas tocopherol content was lower in spelt, suggesting that the higher lipid content of spelt may not be related to a higher germ proportion. Although milling fractionation produced similar proportions of flour and brans in spelt and wheat, it was found that ash, copper, iron, zinc, magnesium, and phosphorus contents were higher in spelt samples, especially in aleurone-rich fine bran and in coarse bran. Even though phosphorus content was higher in spelt than in wheat brans, phytic acid content showed the opposite trend and was 40% lower in spelt versus wheat fine bran, which may suggest that spelt has either a higher endogenous phytase activity or a lower phytic acid content than wheat. The results of this study give important indications on the real nutritional value of spelt compared to wheat. Moreover, they show that the Ca/Fe ratio, combined with that of oleate/palmitate, provides a highly discriminating tool to authenticate spelt from wheat flours and to face the growing issue of spelt flour adulteration. Finally, they suggest that aleurone differences, the nature of which still needs to be investigated, may account for the differential nutrient composition of spelt and wheat.