Background Red blood cell transfusion is associated with morbidity and mortality among adults undergoing cardiac surgery. We aimed to evaluate the association of transfusion with morbidity among pediatric cardiac surgical patients. Methods Patients discharged after cardiac surgery in 2003 were retrospectively reviewed. The red blood cell volume administered during the first 48 postoperative hours was used to classify patients into nonexposure, low exposure (≤15 mL/kg), or high exposure (>15 mL/kg) groups. Cox proportional hazards modeling was used to evaluate the association of red blood cell exposure to length of hospital stay (LOS). Results Of 802 discharges, 371 patients (46.2%) required blood transfusion. Demographic differences between the transfusion exposure groups included age, weight, prematurity, and noncardiac structural abnormalities (all p < 0.001). Distribution of Risk Adjusted Classification for Congenital Heart Surgery, version 1 (RACHS-1) categories, intraoperative support times, and postoperative Pediatric Risk of Mortality Score, Version III (PRISM-III) scores varied among the exposure groups ( p < 0.001). Median duration of mechanical ventilation (34 hours 0 to 493 versus 27 hours 0 to 621 versus 16 hours 0 to 375), incidence of infection (21 14% versus 29 13% versus 17 4%), and acute kidney injury (25 17% versus 29 13% versus 34 8%) were highest in the high transfusion exposure group when compared with the low or nontransfusion groups (all p < 0.001). In a multivariable Cox proportional hazards model, both the low transfusion group (adjusted hazard ratio HR 0.80, 95% confidence interval CI: 0.66 to 0.97, p = 0.02) and high transfusion group (adjusted HR 0.66, 95% CI: 0.53 to 0.82, p < 0.001) were associated with increased LOS. In subgroup analyses, both low transfusion (adjusted HR 0.81, 95% CI: 0.65 to 1.00, p = 0.05) and high transfusion (adjusted HR 0.65, 95% CI: 0.49 to 0.87, p = 0.004) in the biventricular group but not in the single ventricle group was associated with increased LOS. Conclusions Blood transfusion is associated with prolonged hospitalization of children after cardiac surgery, with biventricular patients at highest risk for increased LOS. Future studies are necessary to explore this association and refine transfusion practices.