We report of an previously unpublished combination of partial trisomy 9 and a membranous pulmonary atresia with a large conotruncal ventricular septal defect. The dystrophic female, term newborn presented after delivery with microcephaly, prominent nose and several other facial and skeletal deformities. The echocardiography and angiography showed a membranous pulmonary atresia with ventricular septal defect. Chromosomal analysis revealed a partial trisomy of the short arm with parts of the long arm of chromosome 9 and a small part of the long arm of chromosome 4. A surgical repair of the heart defect was not performed by the known high risk of severe mental retardation of partial trisomy 9. The child died at the age of six months.