Background: The most prevalent type of structural variation in the human genome is represented by copy number variations that can affect transcription levels, sequence, structure and function of genes. Method: In the present study, we used the multiplex ligation-dependent probe amplification (MLPA) technique and quantitative PCR for the detection of copy number variation in 132 intellectually disabled male patients with normal karyotypes and negative fragile-"X"-testing. Results: Ten of these patients (7.6%) showed copy number variation in the subtelomeric regions, including deletions and duplications. Discussion: Duplications of the "SECTM1" gene, located at 17q25.3, and of the "FLJ22115" gene, located at 20p13, could be associated with phenotype alterations. This study highlights the relevance in the aetiology of intellectual disability of subtelomeric rearrangements that can be screened by MLPA and other molecular techniques.