A child with global developmental delay sparing motor skills evolving into later intellectual disability with a consistently normal neuromuscular examination was discovered to have a dystrophin specific mutation in the 3' end of the gene. The deletion in the DMD gene was unsuspected and discovered through array comparative genomic hybridization and confirmed on polymerase chain reaction analysis. This case shows a central nervous system-specific and restrictive phenotype for a disorder that is conceptualized as being progressively neuromuscular in clinical expression. Given the familial and therapeutic implications for accurate diagnosis of DMD mutations, this case raises the possible need for screening boys with global developmental delay/intellectual disability even in the absence of any overt muscle weakness and further shows the utility of comparative genomic hybridization (CGH) analysis in the evaluation of patients with nonsyndromic mental retardation.