Kleefstra syndrome is neurodevelopmental, genetically conditioned disorder, which is characterised by a number of traits, mainly from the neurological system (mental retardation from moderate to severe, childhood hypotonia) and facial dysmorphy. Additionally the following are frequently present: microcephaly, epilepsy, behavioural problems, congenital heart malformations, urorenal defects and obesity. Kleefstra syndrome arises from haploinsufficiency of EHMT1 (the euchromatin histone-lysine N-methyltransferase 1) gene caused by either microdeletions at 9q34.3 or intragenic mutation. Either mutation or deletion (by microdeletions) of the EHMT1 gene results in the defective CNS development. In the present study we report on the case of a girl withcongentialhypothyroidism andKleefstra syndrome proved by genetic examination (a chromosome analysis using the aCHG technique), which showed deletion in the terminal band (9q34.3) of the long arm of chromosome 9, responsible for clinical characteristics of the patient.