To evaluate whether bivalves are contaminated with hepatitis E virus (HEV), samples of a bivalve called Yamato-Shijimi (Corbicula japonica) were examined for HEV by reverse transcription-polymerase chain reaction. Genotype 3 HEV was detected from 2 of 32 packages of Yamato-Shijimi obtained from Japanese rivers, which indicated that HEV contaminates river water in Japan.