Many researches have proven that prolonged endurance exercise like long distance running causes acute, unfavorable effects including damages in kidney, musculoskeletal system, cardiovascular system or gastrointestinal system. Several attempts were made to prevent or modulate these unwanted effects. To better understand the physiological and immunological background of damages caused by prolonged endurance exercise, studies were made on 8 healthy, trained male volunteer during a 2 hour training protocol. The protocol included 1 hour intensive cycling and 1 hour intensive running under medical control. Studies focused on the measurements of clinical chemistry parameters, also on the global gene expression changes of neutrophil granulocytes. Blood samples were collected before exercise (baseline), and 3, 48 and 96 hours following exercise. Based on the results, the intensive physical exercise dramatically changes several parameters in the blood. Many of these parameters return to the baseline within a few hours, while many of them requires several days for the recovery. One of the aims of the future studies is to develop food supplements that may prevent or alleviate the unwanted physiological damages.