Mental retardation (MR) is defined as congenital or early onset lifelong impairment of cognitive and adaptive functioning (IQ < 70). It effects approximately 3% of the Western population. The causes are heterogenous. Numerical or structural chromosome abnormalities are responsible for 10-20% of the mild cases (MMR) and 40% of the severe cases (SMR). Among them Down syndrome represents the most frequent chromosome aberration and the most frequent defined MR syndrome. Gonosomal aberrations do not coincide with MR, as long as only one gonosome is lost or gained. Nearly all unbalanced structural autosomal aberrations cause SMR. Recent studies suggested that sub-microscopic chromosomal microdeletions or subtelomeric rearrangements account for approximately 10% of the undiagnosed cases. They represent a group of newly defined disorders. Single gene mutations are responsible for > 1200 known syndromal conditions with MR. But only few causative genes have been identified as yet. However, an increasing number of genes causing X-linked mental retardation (XLMR) have been localized and cloned, namely 38 genes of the 136 known syndromic conditions and 19 for the non-syndromic conditions. XLMR explains the 20 % excess of males over females. Despite the increasing knowledge about the causes of MR, about half of the cases remain undiagnosed. Guidelines for the diagnostic procedure in children with MR have been proposed.