We report on a 16-year-old girl with tetrasomy 9p mosaicism. Clinical investigations disclosed a malformation syndrome with craniofacial abnormalities, dysplasia of the right clavicle, short neck with cervical ribs, patella dislocation, Dandy-Walker malformation, mental retardation and blindness. Karyotype analysis of blood lymphocytes indicated an additional marker in the size of a C-group chromosome with a large heterochromatic block in 88% of the investigated metaphases. The origin and structure of this additional marker could not be determined by chromosome banding. Application of fluorescence in situ hybridisation and comparative genomic hybridisation identified the origin of the marker chromosome, demonstrating the effectiveness of molecular-cytogenetic investigations in the diagnosis of structural and numerical chromosome abnormalities.