Porcine epidemic diarrhea (PED) is acute viral enteric disease of swine of all ages. Recently, it has been reported that reliable diagnosis is accomplished successfully by monoclonal antibody-based immunohistochemistry (IHC) and in situ hybrydization (ISH). The major objective of this study was to compare IHC with ISH for the detection of PEDV. The techniques were tested on formalin-fixed paraffin-embedded intestinal tissues from 28 piglets naturally infected with PEDV, which were diagnosed by RT-PCR. As its results, PEDV antigens were demonstrated in 12 cases among 28 piglets by IHC. Positive enterocytes were distributed over the tip and along the sides of atrophied or fused villi in the jejunum and ileum. However, PEDV RNAs were detected in 19 cases. Positive cells had dark brown reaction products typically in the cytoplasms of enterocytes. Therefore, ISH was more sensitive than IHC for the detection of PEDV. Furthermore, the reaction of ISH was more strong than that of IHC as the results of testing. These results of this study indicate that ISH could be used as an effective tool for the detection of PEDV.