A 10(6/12)-year-old boy was referred to the genetics department because of mental retardation and dysmorphic findings including microcephaly, flat face, down-slanting palpebral fissures, strabismus, prominent ears, bulbous nasal tip, down-turned corners of the mouth, narrow palate, clinodactyly of the fifth fingers and generalised eczema. Cytogenetic analysis revealed a karyotype of 47,XY,+mar of paternal origin. Multicolour FISH showed the marker chromosome to be derived from chromosome 15. For further elucidation of the phenotype, array-based comparative genomic hybridisation (aCGH) was performed, which revealed dup(5)(q35.2qter) and del(1)(p36.3). Parental FISH analysis revealed that the translocation occurred de novo. Despite the presence of a clinical phenotype along with a microscopically visible chromosomal aberration, a complex cryptic cytogenetic abnormality was causative for the phenotype of the patient. Elucidation of this complex aberration required combination of the whole cytogenetic toolbox. (C) 2008 Elsevier Masson SAS. All rights reserved.