We conducted a cross-sectional study of beta-herpesviruses in febrile pediatric oncology patients (n = 30), with a reference group of febrile pediatric solid-organ transplant recipients (n = 9). One (3.3%) of 30 cancer patients and 3 (33%) of 9 organ recipients were PCR positive for cytomegalovirus. Four (13%) of 30 cancer patients and 3 (33%) of 9 transplant recipients had human herpesvirus 6B (HHV-6B) DNAemia, which was more common within 6 months of initiation of immune suppression (4 of 16 vs. 0 of 14 cancer patients; p = 0.050). HHV-6A and HHV-7 were not detected. No other cause was identified in children with HHV-6B or cytomegalovirus DNAemia. One HHV-6B-positive cancer patient had febrile disease with concomitant hepatitis. Other HHV-6B-positive children had mild "viral" illnesses, as did a child with primary cytomegalovirus infection. Cytomegalovirus and HHV-6B should be included in the differential diagnosis of febrile disease in children with cancer.