The natural course of hepatitis C virus (HCV) carriers is not well understood. We examined the clinical characteristics of individuals exhibiting spontaneous elimination of HCV as part of a cohort study of residents of a HCV hyperendemic area in Japan. In individuals who were judged to have persistent HCV infection in 1995, 302 had at least 4 annual ALT measurements between 1993 and 2000, and had not been treated with IFN. They were tested for the presence of HCV RNA in 2001 and/or 2002 and HCV RNA could not be detected in 20 of the 302 individuals. In these 20 individuals, 7 were confirmed to have detectable HCV RNA and 13 were not until 2000. Thus, 2.4% (7/289) were judged to have spontaneously eliminated the HCV infection during that 6-year period. Although there were no differences in age, sex, ALT levels, or serologically defined HCV genotype between individuals with and without exhibiting spontaneous elimination, there was a significant relationship between the elimination of HCV RNA and a low level of HCVcAg (<20pg/mL) (P<0.001) upon testing in 1995. These results suggest that spontaneous elimination of HCV RNA following persistent infection is rare and appears to be related to viral load.