The purpose of this study was to quantify the effects of selected foot orthoses on muscle activity in the lower extremity during running. Nine male and 12 female recreational runners, clinically and functionally classified as 'pronators', volunteered for this study and performed over-ground running trials at 4m/s in each of four experimental conditions: control, posting, molding, and posting & molding. Electromyographic (EMG) signals were recorded from seven lower extremity muscles. Wavelet analysis was performed to obtain EMG intensities in two frequency bands that were averaged for the pre-heel-strike and post-heel-strike intervals and for 30-100% of stance phase. Posting and custom-molding of foot orthoses increased the global EMG intensity of most muscles of the lower extremity for the stance phase of running (P < 0.05). The increases in EMG intensity were greater in the high- than in the low-frequency bands for some lower extremity muscles (P < 0.05). The effects on muscle activity of posting and custom-molding of foot orthoses differed between the three phases of running gait. The three tested foot orthoses did affect lower extremity muscle activity differently and these effects were specific to the phases of running gait. Combinations of increased requirements of controlling joint motion and minimizing soft tissue vibrations may have led to greater increases in shank muscle activity for the posted condition. The substantial changes in EMG due to orthotic interventions found in this study documents the importance of the study of muscle activity as a reaction to shoe inserts and foot orthoses.