Polymerase chain reaction (PCR) tests for virus in blood and saliva are frequently positive in persons with past infection, re-infection with new strains or latency with or without repeated reactivation of human herpesvirus 6 (HHV6). The aim of this study is to determine the frequency of HHV6 infections in children aged two years or under with an initial diagnosis of fever during an evaluation in the paediatric emergency department of the Children's Medical Center, an Iranian referral hospital, using PCR methodology. In all children, the clinical characteristics noted at the initial evaluation as well as demographic and laboratory findings were obtained. Among 150 patients (91 male, 59 female) admitted to the paediatric emergency department, HHV6 was found in 49 (33%; 14 female [29%] and 35 male [71%]). Rash was seen in 14/49 (29%) of HHV6-positive cases, while 35 cases without rash had a positive PCR test (71%). Seizures were found in 78/150 (52%) patients. There was no significant association between seizures and positive HHV6 results (43% in patients without seizure; 57% in cases that developed seizure). Although standard PCR on samples including blood cannot discriminate between latent and active HHV6 infection, nearly a third of patients (mainly children less than one year old) had HHV6 infection.