FODMAPs present in gluten-containing grains have been identified as a possible cause of gastrointestinal symptoms in people with non-celiac gluten sensitivity, either by themselves, or in combination effect with gluten and other proteins in gluten-containing cereals, such as amylase-trypsin inhibitors (ATIs). The amount of fructans in these cereals is small. In rye, they account for 3.6–6.6% of dry matter, 0.7–2.9% in wheat, and barley contains only trace amounts. They are only minor sources of FODMAPs when eaten in common dietary amounts. Wheat and rye may comprise a major source of fructans when consumed in large amounts.
In a 2018 double-blind, crossover research study on 59 persons on a gluten-free diet with challenges of gluten, fructans, or placebo, intestinal symptoms (specifically bloating) were (borderline) significantly higher after challenge with fructans, in comparison with gluten proteins (P=0.049). Although the differences between the three interventions were small, the authors concluded that fructans are more likely to cause gastrointestinal symptoms in non-celiac gluten sensitivity than gluten. Fructans used in the study were extracted from chicory root, and the results may or may not apply to wheat fructans.
A 2018 review concluded that although fructan intolerance may play a role in non-celiac gluten sensitivity, it only explains some gastrointestinal symptoms. Fructan intolerance does not explain the  extra-digestive symptoms that people with non-celiac gluten sensitivity may develop, such as neurological disorders, fibromyalgia, psychological disturbances, and dermatitis. This review also found that FODMAPs may cause digestive symptoms when the person is hypersensitive to luminal distension.
A 2019 review concluded that wheat fructans could cause certain IBS-like symptoms, such as bloating, but that they are not likely to cause immune activation or extra-digestive symptoms, as many people with non-celiac gluten sensitivity reported resolution of their symptoms after removing gluten-containing cereals. These same participants continued to eat fruits and vegetables with high FODMAP content without issue.