CHARGE syndrome is a genetic disorder caused by a mutation in the CHD7 gene on chromosome 8. Major clinical diagnostic criteria for this heterogeneous disorder include ocular coloboma, choanal atresia/stenosis, characteristic external and internal ear abnormalities, and cranial nerve abnormalities. Patients with CHARGE syndrome often have dysphagia and are at high risk for aspiration of both upper and lower gastrointestinal secretions. The following case-report describes the use of Botulinum toxin A (Botox) to reduce excess salivary secretions in a ventilator dependant infant who would have required a tracheotomy. Thereafter, Botox was used regularly (4–5 months) to decrease the salivary secretions. This case-report is unique in that it describes the intermittent and prospective use of Botox to reduce excess salivary secretions and prevent the resulting aspiration-related complications in an infant with CHARGE syndrome. © 2012 Wiley Periodicals, Inc.