Researchers sought to describe the esophageal microbiota of juvenile patients with esophageal eosinophilia (EE) and those without the condition for a study. In the prospective investigation, biopsies of the esophagus mucosa were taken from 41 children. About 22 had normal esophageal mucosal biopsies (“healthy”), 6 had reflux esophagitis (RE), 4 had PPI-responsive esophageal eosinophilia (PPi-REE), and 9 had eosinophilic esophagitis (EoE). The composition of the microbiome was investigated by sequencing the 16S rRNA gene. The median (range) age in years was 10 (1.5–18), 6 (2–15), 6.5 (5–15), and 9 (1.5–17) for the healthy, RE, PPi-REE, and EoE groups, respectively. The main bacterial phyla were the Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria. Across all groupings, the classes Epsilonproteobacteria, Betaproteobacteria, Flavobacteria, Fusobacteria, and Sphingobacteria were underrepresented. The Vibrionales were prevalent in the healthy and EoE groups but were less prevalent in the RE and PPi-REE groups. The genera Streptococcus, Rahnella, and Leptotrichia accounted for 29.65% of the variation in the data, whereas the genus Microbacterium, Prevotella, and Vibrio explained an additional 10.86%. This was not statistically significant, but the healthy group had a greater diversity and richness score than other categories. The microbiome of the pediatric esophagus was extensive and diverse in both the healthy and sick states. The diversity and richness index of the healthy group was higher than that of other groups, although not by a considerable margin.