Post-transplant lymphoproliferative disorder (PTLD) represents a significant threat to the survival of pediatric transplant recipients. Epstein-Barr (EBV) viral load monitoring using polymerase chain reaction (PCR) has been reported to have a variable sensitively with relatively higher specificity as in an indicator of the development of PTLD. We report two cases of pathologically confirmed PTLD in children who failed to develop sustained increases in their EBV-PCR determined viral loads. We suggest that clinicians should be aware of the potential for false-negative results of EBV-PCR in pediatric transplant recipients.