There have been several reports on the reactivation of human herpesvirus 6 (HHV6) after stem cell transplantation (SCT) in adults, which sometimes induces severe illness. Few reports exist on pediatric patients; therefore, we retrospectively examined HHV6 reactivation after SCT in children. We reviewed 80 patients with a median age of 6 years. We analyzed HHV6 DNA serum samples from the patients before SCT and at 20 and 40 days after SCT using polymerase chain reaction. We also analyzed the relationship between HHV6 reactivation and the syndrome of inappropriate antidiuretic hormone secretion (SIADH). At 20 days after SCT, 35.0% of serum samples were positive for HHV6 DNA. The median viral load was 3.1×10 copies/mL serum. Multivariate analysis showed cord blood transplantation as the only risk factor for HHV6 reactivation. HHV6 reactivation occurs in 59.4% of 32 patients who underwent cord blood transplantation and in 18.8% of 48 patients who underwent SCT from other sources. Among the 14 patients with SIADH, 78.6% experienced HHV6 reactivation. Among the 66 patients without SIADH, only 25.8% had HHV6 reactivation. This result was statistically significant (P<0.001). This analysis revealed that HHV6 reactivation occurs in many children. In addition, HHV6 reactivation plus SIADH should prompt evaluation for central nervous system disease.