RETT syndrome (RS) is a progressive encephalopathy restricted to the female sex. In the present study we investigated 30 females and one male with RS by cytogenetic and molecular-cytogenetic methods. We failed to identify any chromosomal rearangements within the female groups and no correlation between fra(X)(p22) and RS in either the female group or the male. The boy with RS has karyotype 46,XY/47,XXY with abnormal cell clone (47,XXY) in 6–12% of his lymphocytes (revealed by fluorecence in situ hybridization analysis (FISH) of interphase cells with chromosome X-specific DNA probe). Our results indicated a possible connection between RS and X-chromosome replication disturbance. A late-replicating X-chromosome with a specific banding pattern (type ‘C’) has been observed in RS patients only. We propose to analyse the X-chromosome replication pattern as a test for confirmation of RS at preclinical diagnosis.