Marker chromosomes are structurally abnormal chromosomes. It can be super numeral or replace one of the normal chromosomes. Frequently marker chromosomes can be a reason for different abnormalities including intellectual disability. This study is due to molecular cytogenetic of marker chromosome in patient with autism and intellectual disability. Localization of human chromosomes painting probes revealed marker chromosome is derivate from centromeric regions of p- and q-arms of chromosome 15. For accurate study of origination of marker chromosome we have done microdissection of it followed by localization on chromosomes of healthy control and patient. Origination of marker chromosome from chromosome 15 is confirmed. Chromosome 15 is NOR-containing. We localized plasmid containing rDNA on patient chromosomes and detected two clusters if rRNA genes. Ag-NOR-staining revealed both clusters are active. Phenotype forming is discussed.