Genetic variants are considered risk factors for gastric cancer. To date, 61 polymorphisms have been identifed as associated with this disease. The aim of the present study was to analyze the association of some of those polymorphisms with GC in Chile. We performed a case-control study including 310 gastric cancer cases and 311 controls to assess the association of 36 single-nucleotide polymorphisms genotyped by Global Screening Array (GSA). Three polymorphisms was signifcantly associated: PSCA rs2294008 (allele model, OR=1.49, 95%CI 1.17–1.88, P=1.08×10–3), IL-4 rs2243250 (allele model, OR=1.28, 95%CI 1.01–1.62, P=0.04), and MUC1 rs4072037 (allele model, OR=0.78, 95%CI 0.61–0.99, P=0.04).PSCA rs2294008, IL-4 rs2243250 and MUC1 rs4072037 are associated with gastric cancer in Chile. It suggests that those polymorphisms could be used as biomarkers to assess the genetic risk for this cancer outside of the previously studied populations, not only for East Asians and Caucasians populations.