BACKGROUND: Tibial stress fractures are common running related injury and their etiology may include biomechanical factors like impact forces, shock attenuation, lower limb kinematics and how these factors are influenced by intense or prolonged running. Inertial-magnetic measurement units (IMUs) have recently emerged as an alternative to motion capture but their use to date was mostly limited to segmental and joint motion. RESEARCH QUESTION: The present study sought to examine the effects of a prolonged run on shock attenuation, peak tibial and sacral acceleration (PTA, PSA), and lower limb kinematics using IMUs. METHODS: Ten trained male runners (31 +/- 5 yr, 183 +/- 3 cm, 76 +/- 9 kg) performed a twenty-minute prolonged run on an athletic track at estimated lactate threshold speed. Eight IMUs, positioned over the feet, lower and uppers legs, sacrum and sternum, were used to calculate joint kinematics, impact parameters and shock attenuation in the time domain (1-(PSA/PTA)*100). RESULTS: PTA increased while PSA and shock attenuation did not change following the prolonged run. Hip and knee flexion at midstance decreased. Vertical lower leg angle at initial contact did not change. CONCLUSION: By using IMUs, it was shown that a prolonged run at estimated lactate threshold speed had significant effects on kinematics and tibial acceleration parameters. By modifying hip and knee joint kinematics during stance, the body was able to maintain sacral acceleration possibly by shifting from active shock attenuation to more passive mechanisms. SIGNIFICANCE: The present study shows that inertial sensors can be used in outdoor running to measure joint kinematics and kinetic parameters like PTA, PSA and shock attenuation simultaneously. The results of this study show new insights into how the body copes with impact during prolonged running.