Several epidemics of enterovirus 71 (EV71) infections occurred in Taiwan since 1998.We performed the study to determine the changes in cytokine profiles associated with administration of intravenous immunoglobulin (IVIG) in patients with EV71-associated brainstem encephalitis complicated by autonomic nervous system (ANS) dysfunction and pulmonary edema.Plasma cytokine concentrations (IL-1β, IL-6, IL-8, IFN-γ, TNF-α, IL-2, IL-4, IL-5, IL-10, and IL-13) were monitored on admission and within 12–24h after administration of IVIG in a cohort of children (n=22) with virologically confirmed EV71 infection, from March 2000 through April 2004.Plasma levels of IFN-γ, IL-6, IL-8, IL-10, and IL-13 levels significantly decreased in patients with pulmonary edema after administration of IVIG, P<0.05. Plasma levels of IL-6 and IL-8 were significantly decreased in patients with ANS dysregulation after administration of IVIG, P<0.05. Administration of IVIG was not associated with significant changes in plasma concentration of IL-1β, IL-2, IL-4, IL-5 IL-10, IL-13 and TNF-α in patients with ANS dysregulation.These findings suggest that IVIG might be considered to have a therapeutic role in EV71-associated brainstem encephalitis. A clinical trial is needed to support this hypothesis.