CHARGE syndrome is a genetic disorder with multi-systemic congenital anomalies, most commonly including coloboma, heart malformations, choanal atresia, developmental delay, and genital and ear anomalies. The diagnostic criteria for CHARGE syndrome has been refined over the years. However, there are limited reports describing skullbase and craniocervical junction abnormalities. These osseous malformations are often under recognized, especially on MRI. We report here a case of CHARGE syndrome with colobomas, cleft lip and palate, patent ductus arteriosus, undescended testes, and a coronal clival cleft which has not been previously depicted in CHARGE syndrome. The presence of a coronal clival cleft should alert the radiologist to examine the ears, eyes, palate, choana, and olfactory centers for other signs of CHARGE syndrome.