Reverse transcriptase polymerase chain reaction (RT-PCR) and immunohistochemistry (IHC) were used to demonstrate the presence of porcine epidemic diarrhea virus (PEDV) antigen in the intestinal cells of suckling pigs in Luzon. The PEDV antigen was detected in 11 (13.75%) and 32 (40%) out of 80 intestinal samples using RT-PCR and IHC, respectively. RT-PCR generated a 412-bp cDNA probe which amplified the viral RNA encoding the membrane protein of PEDV from the intestinal segments of the jejunum. Immunohistochemistry revealed positive cells in the jejunum as indicated by the brown staining in the cytoplasm of infected cells. Comparative evaluation of the two tests revealed a fair agreement. Histopathological changes observed include vacuolation of enterocytes, villous atrophy as exemplified by 2:1 villous:crypt height ratio and exfoliation of enterocytes which are associated with the clinical signs of PED such as watery diarrhea, dehydration and acidosis. RT-PCR may be used as a screening test for PEDV antigen detection using jejunal tissue with feces because of the shorter duration of processing and testing. IHC, on the other hand, can be performed as confirmatory test using formalin-fixed jejunal samples.