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Intense physical stress, such as that in ultramarathon running, affects the immune system. For monitoring in sports medicine, non-invasive methods, e.g., salivary analysis, are of interest. This pilot cohort study aimed to assess changes in salivary parameters in response to an ultramarathon. The results were compared to blood parameters. Male, healthy finishers (n = 9, mean age: 48 ± 8.8 years, mean height: 1.8 ± 0.1 m, mean weight: 72.5 ± 7.2 kg, mean BMI: 23.5 ± 1.9 kg/cm²) of a 160 km ultramarathon were included. Saliva and blood samples were collected at three time points: T1 (baseline), T2 (shortly after the ultramarathon) and T3 (after recovery). In saliva, cortisol, testosterone, IL-1β, IL-6, IL-8, IL-10, TNF-α, albumin, IgA, α-amylase, aMMP-8, and neopterin were assessed via ELISA. In blood, cortisol, testosterone, IL-1β, IL-6, IL-8, IL-10, TNF-α, blood cell counts, procalcitonin, CRP, osmolality, albumin, and α-amylase were analyzed. The statistical evaluation comprised longitudinal testing and cross-sectional testing between saliva and blood using ratios of T2 and T3 to baseline values. Various parameters in saliva and blood changed in response to the ultramarathon. Comparing blood and saliva, the longitudinal changes of testosterone (p = 0.02) and α-amylase (p = 0.03) differed significantly. Despite the limitations of the study, it underlines that saliva is an interesting option for comprehensive monitoring in sports medicine and necessitates further studies.