The significance of HHV6 DNAemia after solid organ transplantation has not been fully determined. Our objectives were to determine the prevalence of HHV6 DNAemia in pediatric liver transplant recipients and to describe the associated clinical characteristics and outcomes. This was a retrospective case–control study. Eligible liver transplant patients aged ≤ 18 yr with HHV6 DNAemia were matched with two subjects without HHV6 DNAemia. Matching was by age ± 6 months. Among 154 subjects, 25 patients (16%) had HHV6 DNAemia detected by PCR in whole blood or plasma (M:F ratio = 0.9:1). While 28% of subjects with DNAemia (7/25) had symptoms consistent with HHV6 infection, active infection was detected in only four subjects (2.6% of liver transplant patients). The major symptoms/signs were fever, vomiting, lethargy, splenomegaly, bone marrow suppression, and elevated transaminases. The prevalence of DNAemia due to other herpesviruses in cases vs. controls was EBV 56% vs. 60%, CMV 12% vs. 12%, HHV7 20% vs. 12%; p value is not significant for all pairwise comparisons. HHV6 DNAemia in pediatric liver transplant patients is not an uncommon entity. While the clinical relevance is still not entirely established, active HHV6 infection and attributable symptoms are relatively rare.