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The purpose of this study was twofold. Firstly, we evaluated the effect of one-hour running on tibial acceleration parameters. Secondly, we determined whether the shoe fatigue after one-hour running would influence these tibial acceleration parameters. Ten runners ran at a constant preferred speed with a standard running shoe. They also ran one bout of 5 min with another identical but fresh running shoe before and after the one-hour run. Tibial acceleration amplitudes and wavelet analyses demonstrated a significant reduction of the tibial impact parameters after one-hour running, but no significant shoe effect. These reductions could be attributable to the slight increase in stride frequency from the beginning to the end of the one-hour running. Noteworthy, the tibial acceleration reduction was observable along the anteroposterior axis, not along the vertical axis. Considering the tibial acceleration as a potential risk factor for developing running-related injuries, these parameters did not change in a harmful way after one-hour of running at the preferred running speed. The shoe modification during the one-hour run did not seem to influence running biomechanics.