Gastrointestinal symptoms such as diarrhea, cramping, nausea and gastric pain occur frequently in runners during training and competitions. The mechanisms leading to the distress are not fully understood, nor the reason why some remain asymptomatic. However, hyperthermia induced by exercise elevation of core temperature and oxidative damage due to reduced gastric blood flow have been postulated to affect the intestinal epithelial cells. Both sources of stress disrupt the binding of the epithelial tight junction proteins and increase permeability of the membrane to luminal endotoxins. Endotoxins reaching the blood stream through leaky tight junctions lead to an inflammatory response mediated by cytokines. These mechanisms may underlie the gastrointestinal symptoms often experienced by endurance athletes. The aim of this study was to measure running-induced changes in intestinal permeability and inflammatory markers and investigate their association with gastrointestinal symptoms. A secondary objective was to inspect possible correlations between gastrointestinal symptom occurrence and intake of certain nutrients. A total of 17 active runners were allocated into a control group (asymptomatic) or a symptomatic group based on a symptom history questionnaire and completed a 90-minute running test. Intestinal permeability at baseline and after the run were assessed via urine recovery of orally administered Iohexol . LPS (endotoxin) and zonulin concentrations were determined from serum samples. Participants kept a food diary for three days before each measurement and filled out a symptom questionnaire after the run. No significant difference was found in intestinal permeability between symptomatic and asymptomatic runners either at rest or following strenuous exercise. However, both groups experienced a significant increase in intestinal permeability from baseline to after running. LPS concentrations were significantly higher at baseline in the symptomatic group. This may explain the higher symptom occurrence in the symptomatic group. Zonulin levels were higher in control group than symptom group after the run. Zonulin concentration was also higher in the control group after the run compared to baseline. The symptom group reported more stomach pain and stool changes after running compared to controls. Comparison of average intake of various nutrients between the two groups showed no significant differences, indicating an individual predisposition as the cause of symptoms rather than diet alone. The lack of difference in intestinal permeability between the groups combined with the difference in symptom occurrence indicates that intestinal permeability changes alone do not account for symptom development. A possible factor may be individual differences in intestinal mucosa repair ability or some underlying pathology.