Objectives Lymphopenia is a predictor of adverse clinical outcomes in adults with various disease. We sought to determine whether preoperative absolute lymphopenia (absolute lymphocyte count (ALC) less than 4000 cells/���) was an independent predictor of postoperative mortality in children with congenital heart disease. Methods We conducted a retrospective review of medical records of 720 infants who underwent their first cardiac surgical procedure with cardiopulmonary bypass from January 2007 to February 2010. Patients (group A, n=143) who had an ALC of 4000 cells /��� or less were compared with patients (group B, n=577) who had an ALC of greater than 4000 cells /��� using inverse probability of treatment weighting (IPTW) method. Preoperative and intraoperative variables included patient���s age, sex, body weight, Risk Adjusted classification for Congenital Heart Surgery (RACHS-1), use of preoperative inotropes, need for preoperative mechanical ventilation, laboratory results, cardiopulmonary bypass time and cross clamp time. Outcome variables included mortality, dialysis use, NO use, ECMO application, chylothorax, ICU stay duration, hospital stay duration, mechanical ventilation duration, chest tube duration, postoperative 1 day lactate and postoperative 1 day inotrope score. Results There were 421 male (58.5%). 183 patients (25.4%) were neonates at the time of the operation. Group I patients were more likely to be younger, have a lower body weight, low preoperative platelet count, low albumin levels, higher serum creatinine concentrations, more need of preoperative ventilator care, higher inotrope scores and higher RACHS-1 category (P<0.05). Univariate logistic regression models showed that absolute lymphopenia was significantly associated with postoperative early mortality and postoperative dialysis use. (P < 0.05). However, it was not significant when using IPTW method. Meanwhile, absolute lymphopenia affected ICU stay duration, hospital stay duration, mechanical ventilation duration, chest tube duration, postoperative 1 day lactate and postoperative 1 day inotrope score significantly when using T-test and IPTW method. (P < 0.05). Conclusions Preopeartive absolute lymphopenia is a predictor of postoperative morbidiy in infants who undergo congenital heart surgery.