The dietary intake of fermentable oligo-, di- and monosaccharides, and polyols (FODMAPs) can promote gut health, but also trigger gastrointestinal disorders. Wheat as a staple food is considered a major source of FODMAPs in the daily diet. The most abundant FODMAPs in the wheat grain are fructans, which accumulate during plant development in vegetative tissues and are remobilized during grain filling and synthesized in the developing grain. Abiotic stress can foster the accumulation of fructans. Quantification of fructans and/or other FODMAPs is usually carried out by commercial enzymatic assays or by chromatographic methods. There is evidence for genetic variation in fructan accumulation, remobilization efficiency and concentration in the grain. Heritabilities were shown to be moderate to high. Therefore, breeding for low fructan and/or FODMAPs levels in the grain is feasible and was already successfully demonstrated. A significant reduction in FODMAPs of wheat products, however, can be realised by processing. Therefore, long proofing times, especially sour dough fermentation, are most efficient.