It is still uncertain whether intestinal metaplasia (IM) of the esophagogastric junction (EGJ) plays a role in the development of adenocarcinoma of the esophagogastric junction (AEGJ). The purpose of the present study was to clarify the relationship between AEGJ and IM in Japanese patients. Forty-eight AEGJ, <3 cm and centered within 1 cm of the EGJ, were investigated. The frequency of IM around AEGJ and the correlation between IM and clinicopathological features were examined. IM was present in the surrounding mucosa in 22 of 48 cases (46%), and was seen more frequently in older patients (P = 0.008). Lymph node metastasis was observed only in cases in which the tumors were not associated with IM (P = 0.017). The gastric phenotype was seen almost exclusively in the group without IM, while the intestinal phenotype was predominant in the group with IM (P = 0.003). The present study found a lower incidence of associated IM than Western studies, and there were significant differences in clinicopathological features between AEGJ with and without IM. It is suggested that AEGJ may develop via two distinct pathways in Japanese patients: IM-related and IM-unrelated.