Post-transplant lymphoproliferative disease (PTLD) is an abnormal proliferation of lymphocytes that can be a lethal complication in transplant recipients. The risk factors associated with PTLD in pediatric lung transplant recipients are poorly defined. We reviewed the the records of 60 consecutive primary lung transplant recipients with cystic fibrosis (CF) as part of a retrospective cohort analysis. We used univariate and multivariate logistic regression to identify potential risk factors associated with PTLD. A total of 11 of the 60 (18.3%) children were diagnosed with biopsy proven PTLD. Children with CF who were EBV seronegative before transplant (odds ratio: 6.0, 95% confidence interval 1.2, 30.7) and those who experienced three or more episodes of acute graft rejection during the first 90 days following lung transplant (odds ratio: 5.0, 95% confidence interval 1.2, 20.9) were at significant risk for PTLD. There was no interaction between both covariates. Factors that did not increase the risk for developing PTLD included: recipient cytomegalovirus IgG serologic status, induction therapy with anti-lymphocyte(ALG), or anti-thrombocyte globulin (ATG) and the use of ALG, ATG or muromonab-CD3 (OKT3) for steroid-resistant acute graft rejection. Patients with CF who are EBV seronegative prior to lung transplant and/or who have three or more episodes of acute graft rejection during the first 90 days post-transplant have significant risk of developing PTLD. Future studies aimed at surveillance and early intervention for PTLD should focus on this high-risk population.