Exercise-associated physiological disturbances alter gastrointestinal function and integrity. These alterations may increase susceptibility to dietary triggers, namely gluten and a family of short-chain carbohydrates known as FODMAPs (fermentable oligo-, di-, monosaccharides and polyols). A recent surge in the popularity of gluten-free diets (GFDs) among athletes without celiac disease has been exacerbated by unsubstantiated commercial health claims and high-profile athletes citing this diet to be the secret to their success. Up to 41% of athletes at least partially adhere to a GFD diet, with the belief that gluten avoidance improves exercise performance and parameters influencing performance, particularly gastrointestinal symptoms (GIS). In contrast to these beliefs, seminal work investigating the effects of a GFD in athletes without celiac disease has demonstrated no beneficial effect of a GFD versus a gluten-containing diet on performance, gastrointestinal health, inflammation, or perceptual wellbeing. Interestingly, the subsequent reduction in FODMAPs concurrent with the elimination of gluten-containing grains may actually be the factors affecting GIS improvement, not gluten. Pre-existent in the gastrointestinal tract or ingested during exercise, the osmotic and gas-producing effects of variably absorbed FODMAPs may trigger or increase the magnitude of exercise-associated GIS. Research using FODMAP reduction to address gastrointestinal issues in clinically healthy athletes is emerging as a promising strategy to reduce exercise-associated GIS. Applied research and practitioners merging clinical and sports nutrition methods will be essential for the effective use of a low FODMAP approach to tackle the multifactorial nature of gastrointestinal disturbances in athletes.