We investigated the effects of an ultra-marathon on cell-free plasma DNA as well as on mRNA expression of pro-apoptotic (Bax, Bad), anti-apoptotic (Bcl-2) and cell-protective (Hsp70, Hsp27 and Hsp32) genes in mononuclear blood cells (MNCs). Blood samples were drawn from 14 athletes before and immediately after 6-h run. In addition, blood samples were also collected and analyzed 2 and 24 h after the end of the run. Levels of plasma DNA were significantly increased immediately after the marathon (P < 0.001) and were still higher 2 h later (P < 0.005), but significantly lower than those immediately after the race (P < 0.05). Cell-free plasma DNA returned to pre-race levels 24 h after the run. mRNA expressions of Hsp70, Hsp32 and Bax significantly increased in MNCs after the race, whereas Hsp27 and Bad mRNA expression levels showed no significant changes. Bcl-2 expressions decreased immediately after the race (P < 0.001), but increased in the 24 h later (P < 0.05). We conclude that apoptotic ladders of cell-free DNA following exhaustive exercise originate from apoptotic cells and that not only skeletal muscle cells but also leukocytes contribute to this phenomenon.