The purpose of this series of investigations was to determine how custom foot orthotic intervention influences the lower extremity dynamics and intra-limb coordination in healthy and injured female runners. For the first investigation, dynamic data were collected from 12 healthy female runners (Control group) and 12 female runners with a recent history of overuse knee running injury (Treatment group). Results revealed that the influence of CFO intervention on lower extremity appears to occur with short-term intervention. The intervention produced a similar response in both groups. The knee kinematics were not influenced by the intervention however there were changes observed in knee kinetics. For the second investigation, dynamic data were collected during overground running trials in Treatment group from Study One who had completed 6 weeks of orthotic therapy. Data were collected with the subjects running with (CFO condition) and without (Shod condition) foot orthoses in three running shoes with varying midsole composition. Results revealed that the only kinematic variable influenced by running shoe midsole durometer was maximum rearfoot eversion velocity. However, CFO intervention in the footwear led to significant decreases in rearfoot kinematic variables, tibial internal rotation and internal ankle inversion moments. In addition, it was revealed that when a CFO intervention is added to a shoe of lesser density, the dynamics exhibited by the runner are similar to when wearing a shoe of greater density. For the third investigation, kinematic data were collected from 9 healthy female runners (Control group) and 9 female runners with a recent history of overuse knee running injury (Treatment group). Both groups performed a 30-minute treadmill run and relative motion plots were created for the intra-limb couplings. Results revealed that CFO intervention helped to maintain variability during the early stance phase throughout the course of the run in the injured runners. In the Treatment group, the TibTP/CalFP and KnTP/RFFP coordination variability during the early stance phase significantly decreased throughout the course of the 30-minute run for the Shod condition. While wearing the CFO condition the variability went unchanged and better resembled patterns exhibited by the Control group.