From 1996 to 2004, the incidence of Salmonella Javiana infections increased in FoodNet, the U.S. national active foodborne disease surveillance programme. Contact with amphibians and consumption of tomatoes have been associated with outbreaks of S. Javiana infection. To generate and test hypotheses about risk factors associated with sporadic S. Javiana infections, we interviewed patients with laboratory-confirmed S. Javiana infection identified in Georgia and Tennessee during August–October 2004. We collected data on food and water consumption, animal contact, and environmental exposure from cases. Responses were compared with population-based survey exposure data. Seventy-two of 117 identified S. Javiana case-patients were interviewed. Consumption of well water [adjusted odds ratio (aOR) 4·3, 95% confidence interval (CI) 1·6–11·2] and reptile or amphibian contact (aOR 2·6, 95% CI 0·9–7·1) were associated with infection. Consumption of tomatoes (aOR 0·5, 95% CI 0·3–0·9) and poultry (aOR 0·5, 95% CI 0·2–1·0) were protective. Our study suggests that environmental factors are associated with S. Javiana infections in Georgia and Tennessee.