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The endothelial glycocalyx maintains vascular structure and may be subject to shedding during inflammation and also during high-intensive exercise. There are no studies on shedding during ultra-endurance exercise. The "Yukon Arctic Ultra" (YAU) is one of the longest and coldest ultramarathons and its impact on glycocalyx shedding was investigated. Thirteen adults (38.92 ± 8.67 yr, 6 females) of YAU editions 2015-2019 completed 657.03 ± 71.65 km at a moving velocity of 4.17 ± 0.62 km/h. Mean daily temperatures ranged from -12.6°C to -30.5°C. Glycocalyx elements heparan sulfate, hyaluronan, and syndecan CD-138 were quantified from serum at start, 277 km, 383 km, and 690 km. Cortisol, C-reactive protein, creatine kinase, and N-terminal-prohormone of brain natriuretic peptide were also quantified. Seven YAU volunteers (36.14 ± 11.04 yr, 5 females) served as control. There were no time-changes among the control. Among finishers, there was a significant increase for hyaluronan and a significant decrease for syndecan CD-138. Values were greater among female finishers for heparan sulfate at start, 383 km, and 690 km, and among male finishers for hyaluronan at 277 km. Values for syndecan CD-138 were greater among older finishers at all timepoints. There were weak significant correlations ( R 2 < 0.215) between hyaluronan and distance, creatine kinase, and NT-Pro BNP, respectively. Shedding of glycocalyx elements is shown among participants of the YAU. Greater shedding of heparan sulfate among female, greater increases of hyaluronan among male, and greater shedding of syndecan CD-138 among older athletes indicate complex glycocalyx shedding during ultra-endurance exercise. NEW & NOTEWORTHY This is the first study to investigate changes in glycocalyx elements in an endurance footrace and first study to investigate exercise-induced shedding in both sexes. This study comprised of an athlete group who finished the ultra-long distance of up to 690 km during the Yukon Arctic Ultra as well as a control group. Results indicate relevant and different shedding of glycocalyx elements heparan sulfate, hyaluronan, and syndecan CD-138. Sex, age, BMI, and covered distance appear to have an influence on the shedding. Other serum parameters indicative of stress appear to be associated with shedding.