Syphilis is an unexpected diagnosis in the stomach. To establish the diagnosis, evidence of Treponema pallidum in the gastric lesion is necessary. However, it is sometimes difficult to prove the presence of the organisms by conventional methods. The authors describe two cases of early gastric syphilis with pseudolymphomatous histology in which T pallidum gene was detected by the polymerase chain reaction (PCR) using paraffin biopsy sections. The gastric lesion of each case endoscopically and histologically simulated that of malignant lymphoma. However, no clonality was proved by immunohistochemistry or PCR gene rearrangement analysis. No spirochetal organisms were detected with certainty by Warthin-Starry silver stain, whereas the organisms were shown by immunofluorescent stain in one patient. A PCR study showed the treponemal DNA in both patients, and its validity was supported by a direct sequencing and a restriction enzyme digestion. Positive results of serological tests for syphilis and regression of the lesions after antisyphilitic treatment were confirmatory of the diagnosis. Gastric syphilis should be considered as a differential diagnosis when an atypical lymphoid infiltrate fails to show monoclonality. The present PCR method would be helpful in showing T pallidum using routinely processed small biopsy specimens as the tissue source.