Array-comparative genomic hybridisation (array-CGH) and single nucleotide polymorphism array hybridisation (SNP-array) enable genome-wide detection of copy number alterations (CNA). These techniques outperform conventional chromosomal karyotyping in relation to detection of CNAs. The discovery of previously cryptic alterations associated with constitutional or acquired cytogenetic changes with DNA copy number gains or losses quickly led to the identification of novel syndromes or previously unseen tumour-related changes. Array platforms are often targeted to pathognomonic regions to detect well-characterised unbalanced chromosomal rearrangements. Platforms with genome-wide coverage detect additional CNA representing normal genomic variation (copy number variation: CNV) or variation with yet unknown significance. The use of SNP-array facilitating the detection of segmental uniparental disomies might be advantageous compared to classical array-CGH approaches. However, none of the array platforms permit the detection of balanced genomic rearrangements such as translocation, inversion or insertions or some polyploidies. The use of array platforms in cytogenetic testing quickly became a routine diagnostic tool and will replace conventional cytogenetic testing in many instances. In addition, these techniques have the potential to identify genomic changes relevant for the establishment of prognostic stratification of different neoplastic conditions.