Background.The importance of human herpesvirus 6 (HHV-6) as a pathogen in febrile infants ≤90 days of age is unknown.Objective.To determine whether febrile infants 90 days of age and younger evaluated for sepsis have evidence of HHV-6 DNA in plasma or cerebrospinal fluid (CSF).Methods.Febrile infants ≤90 days of age were tested for HHV-6 DNA using a real time quantitative fluorescent probe polymerase chain reaction assay.Results.Eighty samples from 47 infants were tested for HHV-6 DNA; 5 of 47 infants (10.6%) had HHV-6 DNA in plasma. In 2 of the 5 infants with HHV-6 DNA in plasma, HHV-6 DNA was also detected in the CSF. Both infants with evidence of HHV-6 DNA in plasma and CSF had HHV-6 Variant A infection. The quantity of HHV-6 DNA detected ranged from 70 to 169 000 DNA copies/ml. One infant with HHV-6 variant B infection had concomitantEscherichia colibacteremia and urinary tract infection.Conclusions.Approximately 10% of febrile infants ≤90 days of age evaluated for sepsis had evidence of HHV-6 infection. HHV-6 Variant A and B infections were seen in these young infants. HHV-6 DNA was found in infants with and without another explanation for fever. Quantification of viral DNA may be important in determining the relevance of HHV-6 DNA in clinical specimens.