Backgound Array comparative genome hybridisation (CGH) was requested on a 9-year-old boy with mild developmental delay, mild learning difficulties, short stature and dysmorphic features. Methods Array CGH used the BlueGnome Cytochip oligo ISCA 8 × 60K platform. Multiplex ligation probe amplification (MLPA) and fluorescence in situ hybridisation (FISH) were also utilised. Results Array CGH identified a maternally inherited 128 kb interstitial duplication at chromosome Xp21.1 involving exons 10–18 of the DMD gene. FISH indicated that the duplication is located at Xp21. The duplication was confirmed by MLPA and is predicted to cause an in-frame change within the DMD gene. However, his creatinine kinase was normal on two separate occasions. Subsequently, a mutation in the SHOC2 gene was identified which is thought to explain this child’s phenotype. Conclusion The array CGH result is possibly an incidental finding as the SHOC2 gene mutation explains this patient’s symptoms. However, given that this duplication involves an X-linked pathogenic gene, clarification of the clinical significance is required to appropriately manage this patient’s family. Unfortunately, testing of other male family members has not been possible at this time. FISH study is unable to precisely determine if the duplication is within or outside of the DMD gene. This case highlights multiple complex issues in array CGH testing including interpretation of duplications and the importance of correlating the patient’s clinical picture with the array CGH result.