A baby born with esophageal atresia and a laryngeal cleft is presented. Retained salivary secretions and aspiration were a constant management problem whilst the baby was waiting for delayed primary repair of the atresia. The use of anticholinergic agents resulted in thickening of secretions which were difficult to suction and ultimately led to increasing respiratory compromise. Intraglandular salivary gland injection of Botulinum toxin type A was performed using ultrasound guidance. The mean daily salivary flow output prior to treatment was 59 ml. On glycopyrrolate the mean daily salivary output on glycopyrrolate was 16 ml. After Botulinum injection the mean daily salivary output was 7 ml in the 3 weeks after injection. Over the next 14 weeks this increased to 34 ml. There were no adverse effects or significant thickening of secretions after BTX injection. This is the first reported use of Botulinum toxin injection in the management of salivary aspiration in esophageal atresia with laryngeal cleft.