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Background Excessive foot pronation during running in individuals with foot varus alignment may be reduced by medially wedged insoles. Research question This study investigated the effects of a medially wedged insole at the forefoot and at the rearfoot on the lower limbs angles and internal moments of runners with excessive foot pronation and foot varus alignment. Methods Kinematic and kinetic data of 19 runners (11 females and 8 males) were collected while they ran wearing flat (control condition) and medially wedged insoles (insole condition). Both insoles had arch support. We used principal component analysis for data reduction and dependent t-test to compare differences between conditions. Results The insole condition reduced ankle eversion (p = 0.003; effect size = 0.63); reduced knee range of motion in the transverse plane (p = 0.012; effect size = 0.55); increased knee range of motion in the frontal plane in early stance and had earlier knee adduction peak (p = 0.018; effect size = 0.52); reduced hip range of motion in the transverse plane (p = 0.031; effect size = 0.48); reduced hip adduction (p = 0.024; effect size = 0.50); reduced ankle inversion moment (p = 0.012; effect size = 0.55); and increased the difference between the knee internal rotation moment in early stance and midstance (p = 0.012; effect size = 0.55). Significance Insoles with 7˚ medial wedges at the forefoot and rearfoot are able to modify motion and moments patterns that are related to lower limb injuries in runners with increased foot pronation and foot varus alignment with some non-desired effects on the knee motion in the frontal plane.