BackgroundLeaky gut syndrome (LGS) is an idiopathic disorder characterised by alterations in intestinal permeability and low‐grade systemic inflammation. Factors contributing to development of LGS are not well‐understood but physiological stressors such as exercise and transport may play a role which may be of pathophysiological relevance in horses.ObjectivesTo characterise the combined effect of transport stress and exercise on gastrointestinal permeability, and to determine whether these effects are associated with increased inflammatory biomarkers in plasma.Study designControlled, randomised and cross‐over study.MethodsHorses (n = 8 per group) were given a gastrointestinal permeability tracer (iohexol; 5.6% solution; 1 ml/kg bwt) via nasogastric entubation prior to being assigned to a stressed (EX; 1 h of trailer transport immediately followed by 30 min moderate intensity exercise; n = 4) or sedentary control (CON; n = 4) group. Plasma samples were obtained prior to iohexol administration (P1), after transport (P2), at exercise cessation (P3), and at 1 (P4), 2 (P5), 4 (P6) and 8 (P7) hours after cessation of exercise and were analysed for iohexol, inflammatory biomarkers (SAA, LPS, IFABP and LBP) and tight junction proteins (zonulin). Faecal samples were collected at times corresponding to before and after stress from both groups and analysed for zonulin. Data were analysed using a 2‐way RM ANOVA.ResultsIn EX horses, a significant increase in iohexol was observed at P2 (1.5 ± 0.24 μg/ml; p = 0.03), P3 (2.1 ± 0.29 μg/ml; p < 0.001), P4 (2.1 ± 0.17 μg/ml; p < 0.001) compared with P1 (0.7 ± 0.21 μg/ml); iohexol was significantly higher in EX than CON horses at P3 (p < 0.001), P4 (p < 0.001) and P5 (p = 0.003). LPS and SAA were significantly higher in EX than CON at P4 (p < 0.001) and P6 (p = 0.04), respectively.Main limitationsData from our small sample size may not be generalisable to the larger equine population.ConclusionsCombined transport and exercise increases gastrointestinal permeability and systemic SAA and LPS. The model described herein may be useful in further studies on the role of alterations in gastrointestinal permeability in equine disease.