The study aimed at assessing the acute physiological effects of running a 65-km vs a 107-km mountain ultramarathon. Nineteen athletes (15 males and 4 females) from the shorter race and forty three athletes (26 males and 17 females) from the longer race were enrolled. Body weight, respiratory and lower limb strength were assessed before and after the race. Blood samples were obtained before, after and 24-h post-race. Body weight loss did not differ between races. A decrease in squat jump height (p<0.01; d = 1.4), forced vital capacity (p<0.01; d = 0.5), forced expiratory volume in 1 s (p<0.01; d = 0.6), peak inspiratory flow (p<0.01; d = 0.6) and maximal inspiratory pressure (p<0.01; d = 0.8) was observed after the longer race; while, after the shorter race only maximal inspiratory pressure declined (p<0.01; d = 0.5). Greater post-race concentrations of creatine kinase (p<0.01; d = 0.9) and C-reactive protein (p<0.01; d = 2.3) were observed following the longer race, while high-sensitivity cardiac troponin was higher after the shorter race (p<0.01; d = 0.3). Sodium decreased post-competition only after the shorter race (p = 0.02; d = 0.6), while creatinine increased only following the longer race (p<0.01; d = 1.5). In both groups, glomerular filtration rate declined at post-race (longer race: p<0.01, d = 2.1; shorter race: p = 0.01, d = 1.4) and returned to baseline values at 24 h post-race. In summary, expiratory and lower-limb fatigue, and muscle damage and inflammatory response were greater following the longer race; while a higher release of cardiac troponins was observed after the shorter race. The alteration and restoration of renal function was similar after either race.