Abstract: Marker chromosomes are structurally abnormal chromosomes that may be supernumerary in karyotype or replace one of the chromosomes. Marker chromosomes very frequently can be a cause of different pathologies, including a intellectual disability. This study considers the molecular cytogenetic analysis of an acrocentric marker chromosome in a patient with autism and a intellectual disability. With the help of the painting probe localization of human chromosomes, its origin from the pericentromeric regions of the p and q arms of chromosome 15 is shown. For more detailed detection of the region of origin of this chromosome, its microdissection following localization on both healthy control and patient metaphase plates was carried out. Its origin from the nucleolus-containing chromosome 15 is confirmed. Because of the rDNA-containing plasmid localization, two of the ribosome RNA gene clusters were detected on the patient’s chromosomes. Ag-NOR staining showed that both clusters are active. A possible contribution of the revealed chromosome pathology in clinical picture formation is discussed.