The dystrophinopathies, which include Duchenne muscular dystrophy (DMD), Becker muscular dystrophy (BMD), and X-linked dilated cardiomyopathy, are X-linked recessive neuromuscular disorders caused by mutations in the dystrophin gene (DMD). Approximately 70% of mutations causing DMD/BMD are deletions or duplications and the remainder are point mutations. Current clinical diagnostic strategies have limits of resolution that make detection of small DMD deletions and duplications difficult to identify. We developed an oligonucleotide-based array comparative genomic hybridization (array-CGH) platform for the enhanced identification of deletions and duplications in the DMD gene. Using this platform, 39 previously characterized patient samples were analyzed, resulting in the accurate identification of 38 out of 39 rearrangements. Array-CGH did not identify a 191-bp deletion partially involving exon 19 that created a junction fragment detectable by Southern hybridization. To further evaluate the sensitivity and specificity of this array, we performed concurrent blinded analyses by conventional methodologies and array-CGH of 302 samples submitted to our clinical laboratory for DMD deletion/duplication testing. Results obtained on the array-CGH platform were concordant with conventional methodologies in 300 cases, including 69 with clinically-significant rearrangements. In addition, the oligonucleotide array-CGH platform detected two duplications that conventional methods failed to identify. Five copy-number variations (CNVs) were identified; small size and location within introns predict the benign nature of these CNVs with negligible effect on gene function. These results demonstrate the utility of this array-CGH platform in detecting submicroscopic copy-number changes involving the DMD gene, as well as providing more precise breakpoint identification at high-resolution and with improved sensitivity.