Background Primary graft failure, or circulatory insufficiency immediately after transplantation, frequently occurs after pediatric cardiac transplantation and is the most common cause of death after infant transplantation. Risk factors for pediatric primary graft failure are poorly defined. Methods We retrospectively reviewed donor, procedural and recipient characteristics for primary graft failure in 165 pediatric cardiac transplant recipients (median age at transplant 1.1 years) by multivariatle logistic regression. Primary graft failure was defined as the need for mechanical circulatory support or use of multiple intravenous inotrope/pressors, including epinephrine, for circulatory support within the first 24 hours after transplantation. Results Primary graft failure occurred in 54 patients (33%); 24 patients (15%) required mechanical support for their graft failure; and primary graft failure was the cause of death or graft loss in 10 patients. Recipient risk factors associated with an increased risk of primary graft failure included diagnosis of congenital heart disease and a need for mechanical support before transplantation. Ventilator support before transplantation and maximal pulmonary vascular resistance index were risk factors for the development of isolated right ventricular graft failure. Donor risk factors associated with an increased risk for primary graft failure included increasing donor recipient weight and body surface area ratios; increasing donor ischemic time; anoxia as a cause of death; and increasing cardiopulmonary resuscitation time. Donor blood type O+ and hyperdynamic donor systolic function were associated with a decreased risk of primary graft failure. Conclusions Multiple donor, recipient and procedural risk factors, including the type and severity of heart disease in the recipient before transplantation, are associated with primary graft failure after pediatric cardiac transplantation. Avoidance of matching high-risk donors to high-risk recipients may improve morbidity and mortality after transplantation.