During the past ten years a particular molecular technology - array comparative genomic hybridization (aCGH)--has received a great deal of attention. Array CGH can detect simultaneously sub-microscopic copy number changes across the whole genome, thus overcoming the limitations of karyotyping or locus-specific techniques. Array CGH has become an important tool for clinical diagnostics and gene-identification studies and is having a great impact on the understanding of pathologies, the counselling of families and patient management. Different types of array CGH platforms at increasingly higher resolution have been developed, differing mainly in the type of the interrogating probes and in their coverage of the genome. Here, we review the array CGH methodology and its various applications in clinical diagnostics and research. Although it's an expensive technology and differentiating between pathogenic and benign copy number variations is a challenging task, array CGH is an efficient and robust method for assesing disease-causing genomic imbalances and will probably replace karyotype as the primary cytogenetic test.