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Background: The purpose of this study was to investigate the usefulness of salivary cortisol (SC) and eye temperature measured by infrared thermography (IRTET) as biomarkers to manage competitions more effectively and monitor horse welfare in endurance competitions. Based on previous studies, it was hypothesised that pre-exercise baseline SC and IRTET would be higher in younger or less experienced horses, and that post-exercise variation from baseline would be higher in the top finishers. Results: Salivary cortisol measured in 61 competing at qualifier 40 km and 80 km rides showed an abrupt variation (93–256% rise) of the baseline SC levels [median ± interquartile range (IQR) = 0.27 ng/dl ± 0.36] obtained at the Pre-Inspection (PI) into Vet Gate (VG)1 independently of the covered distance, but modest or even lower in the subsequent Vet Gates, e.g. VG2 or VG3. The IRTET measured concomitantly in 16 horses showed significant (p < 0.05) higher levels at the PI in less experienced horses participating in the 40 km ride (median ± IQR = 35.7 °C ± 1.4) than their counterparts in the 80 km ride (median ± IQR = 35.0 °C ± 1.5), but not SC. Baseline SC levels at the PI of horses classifying in the Top5 in the 40 km ride category were significantly (p < 0.05) higher median ± IQR = 0.90 ng/ml ±0.61) when compared to horses positioned from 10th position on (median ± IQR = 0.16 ng/ml ±0.40). A lower IRTET in the PI was correlated with better placement (p < 0.05) and those in the Top5 (median ± IQR = 33.9 °C ± 0.0) had a significantly (p < 0.5) higher variation (+ 10.65%) into the last VG. Conclusion: Pre-exercise baseline IRTET levels, but not SC, were higher in less experienced horses in the 40 compared to their counterparts in the 80 km ride competitions. SC and IRTET showed different indications according to the competition. In the40 km ride competition, higher baseline pre-exercise SC levels seemed to be linked to a better classification outcome. In contrast, in the 80 km ride horses, the higher IRTET variation from pre-exercise into final Vet Gate was the parameter associated with a better performance. A more controlled environment and a larger sample are needed to confirm these results and monitor horse welfare in competitions. [ABSTRACT FROM AUTHOR]