Chromosomal abnormalities are a major cause of mental retardation and congenital malformations. It is known that a considerable fraction of patients with multiple congenital anomalies and mental retardation have submicroscopic chromosomal imbalances. The introduction of whole genome array-CGH allows to investigate the DNA for the presence of copy number alterations with high resolution. In patients with multiple congenital anomalies and mental retardation 15-24% of segmental aneusomies were reported. Given these data, we have decided to apply both classical approaches and innovative methodologies to the study of several patients with mental retardation and congenital anomalies.