Abstract Background/Importance Supraglottoplasty is the surgical procedure of choice for severe laryngomalacia and has shown to be successful in most cases; however, patients with medical comorbidities present a higher rate of failure. To date, the best management of laryngomalacia in children with congenital syndrome remains unclear. Purpose To study the outcome of supraglottoplasty in children with severe laryngomalacia, and to analyze the management and outcome in infants with a congenital syndrome. Methods Retrospective medical records review from January 2003 to October 2012 of all patients who underwent laser supraglottoplasty for severe laryngomalacia at the University Children's Hospital Zurich, Switzerland. Results Thirty-one patients were included; median age at time of surgery was 3.5months. Three patients (10%) had a genetically proven congenital syndrome with associated neurologic anomalies. Overall success rate was 87%. Failures were observed in four (13%) of 31 cases; including all three patients presenting a congenital syndrome. Conclusions Supraglottoplasty is an effective and safe treatment for laryngomalacia in otherwise healthy children. Signs of a possible underlying predominant neurologic origin and discrepancy between the clinical presentation and the endoscopic findings have to be taken into account, as in children with congenital syndrome with neurologic anomalies the risk of failure is higher.