We report on a 13-year-old girl who was the first child of nonconsanguineous parents, and who suffered from short stature accompanied with mental retardation, generalized hyperpigmentation of the skin and craniofacial findings. Her cardiological examination revealed atrial septal defect, mitral valve prolapsus and atrial septal aneurysm. Brain scans revealed dilatation of the third and lateral ventricles and a pontine cleft. Growth hormone (GH) deficiency was observed during the evaluation of GH/IGF-I axis. All the laboratory tests performed including metabolic screening, conventional karyotype and oligonucleotide array were normal. Mutation analysis of the C2ORF3 7 gene revealed no mutation. The clinical signs seen in this patient likely represent a new dysmorphological syndrome which has not been previously described.