Human chromosome 9 is characterized by a high degree of morphologic heteromorphisms, including variation in the size of the heterochromatin. We present a case of a de novo short arm addition of chromosome 9,[46, XY, add(9)(p13)], associated with multiple anomalies, including trigonocephaly, upward slant of the palpebral fissures, patent ductus arteriosus, pulmonary hypertension, hypertrophic cardiomyopathy, umbilical hernia, ambiguous genitalia, and sensorineural hearing and visual loss. This mutation affects the pericentric region of the heterochromatin. This patient exhibited a clinically important breakpoint of the heterochromatic region of chromosome 9 short arm and the associated anomalies.