BACKGROUND: Although both eosinophilic esophagitis (EoE) and Barrett's esophagus (BE) are considered to be associated with T helper (Th) 2-mediated immune responses, the association between EoE and BE is unclear. We investigated the clinical relationship between EoE and BE. METHODS: We conducted a single-center retrospective observational study. The study included 95 patients with EoE and randomly selected age- and sex-matched controls who underwent esophagogastroduodenoscopy during a medical health check-up at Osaka City University in a ratio of 1:2 for comparison. We compared the clinical characteristics and the prevalence rate of BE, reflux esophagitis (RE), hiatal hernia, and atrophic gastritis between EoE patients and controls by univariate analysis. Furthermore, we performed multivariate logistic regression analysis to investigate the association of these factors with EoE. RESULTS: On univariate analysis, the prevalence rate of BE was significantly lower in patients with EoE than in controls (2.1% vs. 13.2%; p = 0.00528). In contrast, the prevalence rate of RE was higher in EoE patients than in controls, but it was not statistically significant (absence and Grades A, B, and C: 74.7%, 18.9%, 5.3%, and 1.1% vs. 83.7%, 12.6%, 3.7%, and 0%; p = 0.193, respectively). Multivariate analysis showed that BE was negatively associated with EoE (odds ratio: 0.132; 95% confidence interval: 0.0302-0.573; p = 0.00686). CONCLUSIONS: BE is negatively associated with EoE in Japanese subjects. The mechanism behind the inverse relationship between EoE and BE should be examined.