Duchenne muscular dystrophy (DMD) is the most common and lethal dystrophy in childhood, caused by mutations in the dystrophin (DMD) gene. Multiplex ligation dependent probe amplification (MLPA) or array comparative genome hybridization (aCGH) is widely used as an initial molecular diagnostic tool. If no deletions or duplications are found in MLPA or aCGH, the samples must be subjected to a second test of direct sequencing. Direct sequencing of the DMD gene, however, is time-consuming, high-cost, and can be inconclusive. Here, we performed whole exome sequencing on a patient with progressive muscle weakness whose MLPA result was negative; the result revealed a rare frame shift mutation. Direct sequencing on the patient's mother showed the same mutation. Whole exome sequencing can be a new diagnostic routine for DMD patients with negative MLPA3.