Enterovirus 71 (EV 71) infections have high neurovirulence and fatality. Immune responses were assessed in 78 patients with EV 71 infection. EV 71 meningoencephalitis occurred more frequently in younger children and in boys. C-reactive protein levels were not elevated, although total leukocyte counts were increased in these patients. The CD40-ligand expression on T cells significantly decreased in children with meningoencephalitis (P=.041). Polymorphism of the cytotoxic T lymphocyte antigen-4 (CTLA-4) at position 49 of exon 1 showed a higher frequency of G/G genotype in patients with EV 71 meningoencephalitis than in those without meningoencephalitis (18/31 vs. 14/47; P=.045) and in control subjects (18/31 vs. 25/93l; P=.007). Specific EV 71 neutralizing antibody titers were detectable but did not differ in children with and without meningoencephalitis in the acute and convalescent stages. Results from this study suggest that younger children with a certain CTLA-4 polymorphism and altered cellular but not humoral response may be linked to EV 71 meningoencephalitis.