Haemophagocytic lymphohistiocytosis (HLH) is a fatal haematological disorder with diverse aetiology. This prospective study was undertaken to characterize HLH cases in Vietnamese children. Clinical and laboratory data, genetic analyses and outcome of the HLH patients were analysed. A total of 33 patients were enrolled from March 2007 to December 2008, with a median age of 3 years. Mutations of the SH2D1A (SAP) and PRF1 genes were detected in one patient, respectively. The virus association was high, up to 63.6% (21/33), including Epstein-Barr virus (19/33), cytomegalovirus (2/33) and dengue virus (2/33). Five patients had malignant lymphoma and two had autoimmune diseases. Twenty-eight patients were treated according to the HLH-2004 protocol. The first response rate was 64.3% (18/28), with an early death rate of 35.7% (10/28). High levels of interferon-gamma, interleukin-10, MIG and interferon-inducible protein-10 (IP-10) were associated with early mortality (P < 0.05). Reactivation among the responders was high (9/18) and the uneventful resolution was low (3/18) after a median follow-up of 35 weeks. In conclusion, the majority of HLH cases are associated with virus infections in Vietnamese children. Familial HLH is rare. The frequent reactivation and high mortality demands a more appropriate therapeutic regimen in tropical areas like Vietnam.