We investigated the relationship of H. pylori stratified by cytotoxin-associated gene A (cagA) status with nonalcoholic fatty liver disease (NAFLD) in the general population of the United States (US). We utilized the Third National Health and Nutrition Examination Survey from 1988 to 1994 in this study. NAFLD was defined by ultrasonographic detection of hepatic steatosis in the absence of other known causes of liver diseases and significant alcohol consumption. Hepatic steatosis was assessed by parenchymal brightness, liver to kidney contrast, deep beam attenuation, bright vessel walls and gallbladder wall definition. Antibodies to H. pylori and cagA of participants were measured using H. pylori IgG and anti-cagA IgG enzyme-linked immunosorbent assays. Among 5,404 participants, the prevalence of NAFLD was higher in H. pylori positive subjects (33.5±1.8%) compared to H. pylori negative subjects (26.1±1.7%, p <0.001). In terms of cagA protein status stratification, while cagA positive H. pylori group did not demonstrate an association with NAFLD (OR: 1.05; 95% CI: 0.81–1.37), cagA negative H. pylori group was noted to have a significant association with NAFLD in a multivariable analysis (OR: 1.30; 95% CI: 1.01–1.67). In conclusion, our study demonstrated that cagA negative H. pylori infection was an independent predictor of NAFLD in the US general population.