Detailed laboratory tests help to evaluate the body condition of athletes who accomplish marathon distance, choose right means of recovery, and thus prevent the development of pathology. The biochemical parameters of blood were described at rest, after finish and after 24 h of recovery. The opening of mitochondrial permeability transition pores as a possible marker of muscle fatigue was tested as mitochondrial factor release (increased OD of blood serum in UV diapason). Our results showed that biochemical markers that need to be controlled in amateur marathon runners include metabolism regulation indicators–aspartate aminotransferase activity (GOT), total creatine kinase (CK NAK), and their rafio (CK NAK/GOT). The GOT level significantly increased by 1.8 times after the marathon and by 2.4 times after 24 h of recovery. The level of CK NAK and CK NAK/GOT rafio after 24 h of recovery increased by 11.7 and 4.8 times, respectively. The increased activity of sarcoplasmic GOT and CK NAK enzymes, the CK NAK/GOT rafio can indicate the likelihood of skeletal muscle damage. The mitochondrial factor was not detected in the blood neither in resting-state nor after marathon running. These data support the conclusion made after analysis of the biochemical indexes about the satisfactory energy balance of amateur athletes tested.