To determine if human papillomavirus (HPV) infection could be associated with the development of adenocarcinoma of esophagogastric junction (AEG).A total of 106 consecutive AEG patients and 59 consecutive gastric carcinoma patients who accepted surgery at our department between January 2004 and December 2006 were selected. Specimens from tumors and uninvolved mucosa were obtained intra-operatively. Genomic DNA was extracted by the phenol-chloroform-isoamyl alcohol extraction protocol. The HPV infection was determined by PCR using primer set SPF1 and GP6+. Specificity of the amplified products was confirmed by sequencing.The HPV infection rates in AEG and gastric cancer were 10.4% (11/106) and 10.2% (6/59) separately (P = 0.966).HPV is not a major factor in the carcinogenesis of AEG type II, AEG type III or stomach.