Epstein–Barr virus (EBV) is the most common infectious cause of non-genetic hemophagocytic lymphohistiocytosis (HLH). To investigate EBV-infected lymphocytes and immune dysfunction in EBV-associated HLH, blood samples from a 6-year-old boy were longitudinally analyzed using molecular techniques. EBV-positive lymphocytes were detected as CD5+, CD8+, and/or HLA DR+ lymphocytes on Day 25 of the disease, mostly disappearing thereafter. CD8+ cells specific for lytic antigen BRLF1 were detected, but cells specific for latent antigens EBNA3 and LMP2 were not. EBV genes EBNA1, LMP1, LMP2, EBER1, BARTs were detected, suggesting a latency type II gene expression pattern in this case. Pediatr Blood Cancer 2013;60:326–328. © 2012 Wiley Periodicals, Inc.