PTLD is an important complication following heart transplantation. To better define the risk factors of PTLD in children, we performed a case–control study. All pediatric cardiac transplant recipients who developed their first episode of PTLD were matched by age (±1 yr) and time since transplant (±1 yr) with those who did not. PTLD occurred in nine of 95 cardiac transplant recipients (9%), 0.3–7.8 yr following cardiac transplantation (median = 2.5 yr). Patients were 0.1–16.4 yr (median = 3.7) at transplantation. Biopsies revealed polymorphic B cell hyperplasia (three), polymorphic B cell lymphoma (one), monomorphic diffuse large cell B cell lymphoma (three) and monomorphic Burkitt's-like lymphoma (two). Patients who developed PTLD were at no greater risk of death (p = 0.31). Recipient EBV seronegativity at time of transplant (p = 0.08), EBV seroconversion (p = 0.013) and recipient CMV seronegativity (p = 0.015) were associated with the development of PTLD by conditional logistic regression; sex, race, donor age, recipient diagnosis, donor CMV seropositivity, recipient treatment for CMV infection, EBV seropositivity at the time of PTLD diagnosis, and number of rejection episodes, treated rejection episodes, and lympholytics used were not. There was no significant association between PTLD and death in our recipients. EBV seroconversion and recipient CMV seronegativity were associated with the development of PTLD.