Intellectual disability is affecting 3.0-4.0% of the general population. Copy number variants (CNVs) are a significant cause leading to neurodevelopmental disorders such as intellectual disability, epilepsy, autism spectrum disorders and developmental delay. The use of single nucleotide polymorphism (SNP)-array and array comparative genomic hybridization (aCGH) as diagnostic tools has led to the recognition of new microdeletion/microduplication syndromes associated with neurodevelopmental disorders. It is also useful for further characterization of marker chromosomes. Here, we report a girl with mild intellectual disability and mild facial dysmorphisms. Cytogenetic analysis showed a marker chromosome in some percent of the cells and was followed by SNP-array karyotyping that detected, in addition, a 9655 Mb de novo interstitial deletion at 9q21.1-9q21.2.