Monitoring of Epstein-Barr virus DNA viral loads (EBVL) in whole blood and plasma following pediatric kidney transplantation has been routinely employed to facilitate the diagnosis and management of Epstein-Barr virus (EBV) infection. However, recent studies from our laboratory and others have demonstrated a number of transplant recipients with chronically high EBVL, thereby calling into question the clinical utility of monitoring EBVL. The aim of this study was to compare the relative diagnostic value of measuring EBV DNA load in plasma and whole blood collected in parallel from 64 pediatric kidney transplant recipients. Thirteen patients had a high EBVL and were characterised in detail and 11 (84.6%) of these were EBV seronegative at the time of kidney transplant. It has been hypothesised that the point immediately before EBV seroconversion can be identified by a peak in plasma EBVL. However, compared to plasma, whole blood EBVL remained fairly constant over time for these patients. Overall, a correlation was observed between whole blood and plasma EBVL in sequential specimens collected post-transplant (r=-0.95, p<0.002), however, there was no consistent ratio between the EBVL and individual time-point EBVL between the two sample types. Our findings indicate that the optimal sample type may vary in different states of infection; however the detection of EBVL, in particular a significant increase in EBVL, provides a clinical trigger to investigate the patient in more detail.