Adenoviral (AdV) infections after transplantation remain a challenge in pediatric patients. Qualitative and quantitative PCR offer new approaches to early diagnosis and monitoring. However, their role in the management of AdV infections in pediatric transplant recipients remains to be determined. We report six children with positive qualitative serum-PCR for AdV on routine follow-up after transplantation (liver n = 4, hematopoetic stem cells (HSCT) n = 1, combined liver and HSCT n = 1). None of these children were symptomatic at the time of first detection of AdV. Two patients remained asymptomatic, one developed hemorrhagic cystitis and enteritis. Three children with positive PCR developed high viral load on quantitative PCR, all developed clinical AdV sepsis with further rising virus load. Despite antiviral therapy with cidofovir, these three patients died of septic multiorgan failure. Positive qualitative AdV-PCR from blood after pediatric transplantation is not necessarily followed by clinical disease. In case of positive AdV-PCR, monitoring by serial quantitative PCR is useful regarding treatment decision and prevention of fatal disease.