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Background and Aim: Foot orthoses are widely prescribed to treat a range of lower extremity problems. Long-term biomechanical effects of foot orthosesare not clearly documented in the literature. The aim of this study was to examine long-term effects of foot orthoses on leg muscles activity in individuals with pesplanus during walking. Materials and Method: In this clinical trial we selected 45 subjects after clinical examination. The subjects were divided into three equal groups: experimental pesplanus, control pesplanus and a healthy control group (with normal feet). In the pre-test stage, electrical activity of leg muscles including tibialis anterior, peroneus longus, medial gastrocnemius and soleus were recorded at stance phase of walking, while all subjects walked barefoot along a 14m line. Experimental pesplanus group wore the custom-made orthoses for a period of six months. Then experimental pesplanus and control pesplanus groups underwent post-test. One-way ANOVA was used for data analysis. Results: After six months of utilizing foot orthoses, the tibialis anterior activity significantly decreased in contact sub-phase (P=0.006). The medial gastrocnemius activity showed a significant decrease in midstance sub-phase in the post-test (P=0.007). Also, the soleus muscle had decreased activity in contact (P=0.033) and midstance (p=0.023) sub-phases in the post-test. Conclusion: According to the results of this study, we found that long term use of foot orthoses could change muscle activation and result in secondary adaptation. Received: Jan19, 2013 Accepted: Oct 8, 2013 Conflict of interest: None declared