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Background: In Arizona <i>Helicobacter pylori</i> prevalence of infection among Navajo adults is about 62% and gastric cancer incidence rate is 3–4 times higher than that of the non-Hispanic White population. Aim: The aim of this study was to estimate the prevalence of specific <i>H. pylori</i> virulence factors (<i>cagA</i> and <i>vacA</i>) among Navajo patients undergoing and their association with gastric disease. Methods: Virulence genes, <i>cagA</i> and <i>vacA,</i> in <i>H. pylori</i> were investigated in gastric biopsies from 96 Navajo patients over age 18 who were undergoing esophagogastroduodenoscopy. Biopsies from the antrum and fundus were used for molecular characterization to determine <i>cagA</i> type and number of EPIYA motifs and presence of alleles in the signal (s) and medium (m) regions of the <i>vacA</i> gene. Results: <i>H. pylori</i> infection was found in 22.9% of the biopsy samples. The <i>cagA</i> gene amplified in 57.6% of samples and showed a predominant “Western <i>cagA</i>” type, with the EPIYA-ABC motif (45.4%), most prevalent. The <i>vacA</i> allele s1bm1 was the most prevalent (54.5%). Conclusions: <i>H. pylori</i> genotypes were predominantly <i>cagA</i> Western-type and ABC EPIYA motifs. The <i>vacA</i> s1bm1 genotype was the most prevalent and seemed to be associated with gastritis. American Indian/Alaska Native populations are at higher risk for gastric cancer. It is important to identify genotypes of <i>H. pylori</i> and virulence factors involved in the high prevalence of <i>H. pylori</i> and associated disease among the Navajo population.