Background: Perioperative advances have led to significant improvements in outcomes after many complex neonatal open heart procedures. Whether similar improvements have been realized for the modified Blalock-Taussig shunt, the most common palliative neonatal closed-heart procedure, is not known. Methods: Data were abstracted from The Society of Thoracic Surgeons Congenital Heart Surgery Database (2002 to 2009). Inclusion criteria were all neonates who received a modified Blalock-Taussig shunt with or without cardiopulmonary bypass, and with or without concomitant ligation of a patent ductus arteriosus. Discharge mortality was the primary end point. A composite morbidity end point one or more of the following: postoperative extracorporeal membrane oxygenation, low cardiac output, or unplanned reoperation. Associations with patient and procedural variables were assessed with univariable and multivariable analyses. Results: The inclusion criteria were met by 1273 patients. The discharge mortality rate was 7.2%, and composite morbidity, as defined, was 13.1%. Primary diagnoses were classified as (1) those potentially amenable to biventricular repair (62%), (2) functionally univentricular hearts (22%), and (3) pulmonary atresia with intact ventricular septum (PA/IVS; 14%), and miscellaneous (2%). Discharge mortality stratified by primary diagnoses was PA/IVS (15.6%), functionally univentricular hearts (7.2%), and diagnoses potentially amenable to biventricular repair (5.1%). Need for preoperative ventilatory support, diagnosis of PA/IVS or functionally univentricular hearts, and any weight less than 3 kg, were risk factors for death. Preoperative acidosis or shock (resolved or persistent) and diagnosis of PA/IVS or functionally univentricular hearts were predictors of composite morbidity. Nearly 33% of the deaths occurred within 24 hours postoperatively, and 75% within the first 30 days. Conclusions: The mortality rate after the neonatal modified Blalock-Taussig shunt remains high, particularly for infants weighing less than 3 kg and those with the diagnosis of PA/IVS.