The risk allele of a single nucleotide polymorphism (SNP) rs2294008 in the
Prostate stem cell antigen
(
PSCA
) gene is strongly associated with gastric cancer. Although the Kyoto classification score is believed to be an indicator of gastric cancer risk, it lacks supporting genetic evidence. We investigated the effect of this risk allele of
PSCA
SNP on the Kyoto score. Participants without a history of gastric cancer or
Helicobacter pylori
(
H. pylori
) eradication underwent esophagogastroduodenoscopy,
H. pylori
evaluation, and SNP genotyping. The Kyoto score is the sum of scores obtained from endoscopy-based atrophy, intestinal metaplasia, enlarged folds, nodularity, and diffuse redness. The Kyoto score is novel in the light of scoring for gastritis. A total of 323 patients were enrolled (number of individuals with genotype CC: 52; CT: 140; TT: 131, average age: 50.1 years, male: 50.8%). The patient baseline characteristics including age, sex, body mass index, smoking, drinking, family history of gastric cancer, and
H. pylori
status had no association with
PSCA
SNP. The Kyoto score was higher in T (CT or TT genotype; risk allele) carriers than in CC carriers. Atrophy, enlarged folds, and diffuse redness scores were higher in T allele carriers (risk allele) than in CC genotype individuals. In multivariate analysis, the Kyoto score was independently associated with
PSCA
SNP (OR: 1.30,
p
= 0.012). Thus, the Kyoto score was associated with a genetic predisposition.