Aim of review. To present up-to-date data on microbiome role in development of various esophageal diseases and options of probiotics application in esophageal diseases treatment. Summary. Gastro-intestinal microbiome is an invisible organ of our body integrating about 1014 microorganisms. Main bacteria types for the esophagus are Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Fusobacteria and TM7. The microbiome of the normal esophageal mucosa is represented by gram-positive bacteria like Firmicutes; microbiome in patients with Barret's esophagus and esophagitis is constituted mainly by gram-negative anaerobe bacteria: Bacteroidetes, Proteobacteria, Fusobacteria and Spirochaete; patients with eosinophilic esophagitis have Proteobacteria. Expression of tumor and inflammatory mediators (toll-like receptors, interleukins, nuclear factor κB, cyclooxygenase-2) can be determined by microbiome pattern. Conclusion. Results of original studies demonstrate microbiome changes of the esophagus at gastroesophageal reflux disease, Barret's esophagus, adenocarcinoma of the esophagus and eosinophilic esophagitis. Toll-like receptors, cytokines, nuclear factor κB, cyclooxygenase-2 can be potential mediators of inflammation and carcinogenesis which expression can be modified by microbiome spectrum. Probiotics can become the priority trend in treatment of diseases of the esophagus.