MiRNA is a group of endogenous short non-coding RNAs which may modulate the expression of more than 60% protein coding genes. MiRNAs have been confirmed to play an important role during the development of muscle and disturbance of miRNA profile has been found in the tissue or serum sample of patients with amyotrophic lateral sclerosis (ALS) and Duchenne muscular dystrophy (DMD). Herein, we detected 14 candidate miRNAs in the serum samples from Hirayama disease (HD) patients. We found the expression of miR-423 was significantly reduced and miR-206 was up-regulated in HD patients. Predicted by bioinformatics tools, confirmed by dual luciferase assay and immunoblotting, we identified that MSTN is a direct target of miR-423 and the target region is conserved between human and mouse. Functional study in mouse myoblasts C2C12 indicated that reduced miR-423 contributes to decreased cell proliferation. To our knowledge, we constructed the relationship between miRNA and HD pathogenesis for the first time and provide a potential new biomarker for HD clinical diagnosis.