Objective To detect subtle mutations in the dystrophin gene by exome capturing using second-generation sequencing technique. Methods Exome capturing using second-generation sequencing technique was used to detect mutations of dystrophin gene in a patient with typical clinical manifestations of Duchenne muscular dystrophy （DMD）, but without deletions or duplications in the dystrophin gene. The mutations were verified by Sanger sequencing, and bioinformatics was employed to predict its influence on the coding. The patient’s mother and 100 healthy volunteers were taken as controls.Results A base change in the first base of intron 50 (G>C) was found in dystrophin gene of the patient, and his mother was heterozygosis at the same site. Bioinformatics predicted that the 5′ donor splicing site of intron 50 would disappear due to this base change, which would alter the amino acid sequence at the C terminal of corresponding peptide and result in the appearance of premature termination codon. Sanger sequencing confirmed that the base change was a novel pathogenic mutation in the dystrophin gene, and it was absent in normal controls. Conclusion It is demonstrated that exome sequencing technique can effectively detect the subtle mutations in the dystrophin gene, which may contribute to better molecular diagnosis of DMD.