Objective:This study aimed to introduce droplet digital PCR (ddPCR) for monitoring Epstein-Barr virus (EBV) infection after allogeneic hematopoietic stem cell transplantation (alloHSCT) in children and assess its viability as a complementary detection method in clinical settings.Methods:A total of 290 blood samples from 47 children undergoing alloHSCT were collected. Both ddPCR and real-time quantitative PCR (qPCR) were employed to detect EBV DNA load in plasma, with a comparison of detection efficiencies between the two methods. Continuous monitoring of 39 children was conducted to observe dynamic changes in EBV DNA load in plasma and analyze the merits and drawbacks of both methods.Results:The EBV positive detection rate of ddPCR was significantly higher than that of qPCR ( χ2=20.25, P<0.001), particularly in samples with low viral loads. Among the children monitored continuously for EBV DNA, 14 out of 39 exhibited positive ddPCR result. Notably, in two cases where patients displayed rash and fever symptoms with positive ddPCR result but negative qPCR result, ddPCR demonstrated heightened sensitivity in early EBV infection detection. Conclusions:ddPCR holds certain advantages in monitoring EBV infection post-alloHSCT in children, especially for samples with low viral loads. However, as this method is still in the exploratory stage of clinical application, further research and practice are needed to validate its utility.