We investigated the change of body composition in ultra- endurance runners during a multi-stage ultra-endurance run, the Isarrun 2006 in Bavaria, Germany, where athletes had to run 338 km within 5 days. Body mass, skin fold thicknesses and circumferences of extremities were measured in 21 well-experienced extreme endurance male runners (mean ± SD, 41.5 ± 6.9 years, 72.6 ± 6.4 kg, 178 ± 5 cm, BMI 23.0 ± 2.0 kg·m^-2), who finished mainly within the first half of the ranking, in order to calculate skeletal muscle mass and body fat mass to prove changes after the race. Body mass and calculated fat mass did not change significantly (p>0.05), but, calculated skeletal muscle mass decreased significantly (p<0.05) by 0.63 ± 0.79 kg by the end of the race. The most apparent decline (p<0.01) of the calculated skeletal muscle mass was during the first stage, and no changes were observed during the last 4 stages. We conclude, that a multi- stage ultra-endurance run over 338 km within 5 days leads to no changes of body mass or body fat mass, but a statistically significant decrease of skeletal muscle mass of 0.63 ± 0.79 kg by the end of the race in well-trained and well-experienced ultra-endurance runners. The change of skeletal muscle mass has to be evaluated in further studies at ultra-endurance races with suitable methods to detect changes in hydration status and water metabolism.