In order to simplify dengue and Japanese encephalitis (JE) IgM-ELISA, we have been trying to produce antigens as infected C6/36 cell culture fluid. In this study, we examined the effect of nonionic detergents, which were used to inactivate viral infectivity, on dengue and JE antigen titers as well as the results in an IgM-capture ELISA. In the antigen detection ELISA, antigen titers were not significantly reduced after treatment with nonionic detergents (Nonidet P-40 or Triton X-100, at 0.01 to 0.1% final concentration). In contrast, in the IgM-capture ELISA, the color development was significantly reduced when the antigens were pretreated with nonionic detergents. The results suggest that certain epitopes which react with anti-viral IgM antibodies, but not IgG antibodies, have been destroyed by treatment with nonionic detergents. The results indicate that we cannot use nonionic detergents to inactivate the infectivity of assay antigens.