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A model of the lower extremity was created and analyzed to estimate the magnitude of the loads at common injury sites during running and the proportions due to muscle and ground reaction forces. The range of peak loads, normalized to subject body weight (BW), estimated from five running trials were: (1) Achilles tendon force: 6.1–8.2 BW; (2) ankle bone-on-bone—compressive force: 10.3–14.1 BW; shear force: −0.4− −0.7 BW; (3) lower leg—compressive force: 10.3–14.1 BW; shear force: −0.4− −0.7 BW; bending moment: −85− −117 N·m; (4) patellar tendon force: 4.7–6.9 BW; (5) patellofemoral joint compressive force: 7.0–11.1 BW; (6) plantar fascia force: 1.3–2.9 BW. All peak loads were associated with mid-stance and push-off when muscle activity was maximal. The impact force at heel contact was estimated to have no effect on the peak force seen at the chronic injury sites. The plantarflexor muscles were shown to provide an anti-shear mechanism at the ankle and an anti-shear, anti-bending mechanism within the lower leg. Simple sensitivity analyses were performed on the models to display possible variability in the peak load estimates.