Each year, esophageal and gastric cancers cause more than 900,000 deaths worldwide. Human papilloma virus (HPV), especially type 16, has been suggested to have a role in the etiology of esophageal cancer, however, the results of previous seroepidemiological studies have not been consistent. We conducted a large prospective study to examine the association between serum antibodies to HPV 16, HPV 18 and HPV 73 and subsequent development of esophageal squamous cell carcinoma (ESCC), gastric cardia adenocarcinoma (GCA), and gastric noncardia adenocarcinoma (GNCA) in a high-risk population for these cancers in Linxian, China. Case and control subjects for this study were selected from the 29,584 participants of the Linxian General Population Trial. Prediagnostic serum samples from 99 cases of ESCC, 100 cases of GCA, 70 cases of GNCA, and 381 age- and sex- matched controls were selected for this study. The presence of antibodies to HPV virus-like particles was determined by type-specific enzyme-linked immunosorbent assays. Fewer than 15% of ESCC, GCA, or GNCA cases were positive for each HPV type, and no significant associations were found. The adjusted odds ratios (ORs) and 95% confidence intervals (95% CIs) for HPV 16 seropositivity and ESCC, GCA, and GNCA risk were 1.6 (0.8–3.3), 1.3 (0.6–2.8) and 0.4 (0.1–1.6), respectively. The comparable ORs (95% CIs) for HPV 18 were 1.0 (0.4–2.2), 0.9 (0.4–2.1) and 1.5 (0.6–3.4). For HPV 73, these figures were 1.3 (0.6–2.5), 1.2 (0.6–2.3) and 0.9 (0.4–2.1). The results of this study do not support a major role for HPV 16, HPV 18 and HPV 73 in the etiology of esophageal and gastric cancers in Linxian, China.