Detection of the ethiological factors for congenital abnormalities and/or mental retardation is a challenge for the clinician. In a substantial part of patients the disease is due to microstructural chromosomal copy number changes invisible by bright field cytogenetic analysis. This class of diseases is known as microdeletions/ microduplications or contiguous gene syndromes. We have studied two groups of children with clinical signs of Williams-Beuren and DiGeorge syndromes. We have performed cytogenetic analysis and FISH with locus specific probes for WBS and DGS. In two cases with DGS the deletion of the critical region on 22q was visible on bright field microscopy. In all other patients the caryotypes were normal. Using FISH a microdeletion of ELN1 locus was found in 8 out of 14 patients with WBS and a microdeletion of TUPLE1 was found in 7 out of 16 patients with DGS. In our groups of patients there is some prevalence of males (19 males / 11 females). They are more frequently affected by congenital heart abnormalities. Therefore they have the diagnosis earlier then the females.