This study investigated the effects of a high carbohydrate diet, with varied fermentable oligo-, di-, and mono-saccharide and polyol (FODMAP) content, before endurance exercise on gastrointestinal integrity, motility, and symptoms; and subsequent exercise performance. Twelve endurance athletes were provided with a 48 h high carbohydrate (mean±SD: 12.1±1.8 g kg day-1) diet on two separate occasions, composed of high (54.8±10.5 g day-1) and low FODMAP (3.0±0.2 g day-1) content. Thereafter, participants completed a 2 h steady-state running exercise at 60% of (22.9±1.2 °C, 46.4±7.9% RH), followed by a 1 h distance performance test. Pre-exercise and every 20 min during steady-state exercise, 100 mL maltodextrin (10%w/v) solution was consumed. A 150 mL lactulose (20 g) solution was consumed 30 min into the distance performance test to determine orocecal transit time (OCTT) during exercise. Blood was collected pre- and post exercise to determine gastrointestinal integrity biomarkers (i.e., I-FABP, sCD14, and CRP). Breath hydrogen (H2) and gastrointestinal symptoms (GIS) were determined pre-exercise, every 15 min, during and throughout recovery. No differences in gastrointestinal integrity biomarkers, OCTT, or distance completed were observed between trials. Pre-exercise total-GIS (1.3±2.9vs. 4.3±4.4), gut discomfort (9.9±8.1vs. 15.8±9.0), and upper-GIS (2.8±2.6vs. 5.7±4.8) during exercise were less severe on high carbohydrate low FODMAP (HC-LFOD) versus high carbohydrate high FODMAP (HC-HFOD) (p<0.05). Gut discomfort (3.4±4.4vs. 0.2±0.6) and total-GIS (4.9±6.8vs. 0.2±0.6) were higher during recovery on HC-LFOD versus HC-HFOD (p<0.05). The FODMAP content of a 48 h high carbohydrate diet does not impact gastrointestinal integrity or motility in response to endurance exercise. However, a high FODMAP content exacerbates GIS before and during exercise, but this does not impact performance outcomes.