The molecular karyotype or aCGH is a powerful cytogenetic diagnostic tool that allows detection of losses and gains of genetic material. Thanks to their high resolution, the aCGH has a diagnostic yield up to 100 times bigger than the conventional karyotype, depending on the design. This increased diagnostic yield makes the aCGH a first choice diagnostic tool for patients with autism, developmental disorders, intellectual disability and multiple congenital anomalies, pathologies related to a high number of chromosomal rearrangements and CNVs.