The gut microbiota may be considered a crucial "organ" of human body because of its role in the maintenance of the balance between health as well as disease. It is mainly located in the small bowel and colon, while, the stomach was long thought to be sterile in particular for its high acid production. In particular, stomach was considered "a hostile place" for bacterial growth until the identification of Helicobacter pylori (HP). Now, the stomach and its microbiota can be considered as two different "organs" that share the same place and they have an impact on each other. Indeed, microscopic structures of gastric mucosa (mucus layer and luminal contents) influence local microflora and vice versa. In this article our attention is directed specifically to explain the effects of this "cross-talk" on gastric homeostasis. Gastric microbiota mainly consists of two general groups, namely HP and non-HP bacteria. Here, the relationship between these two populations will be reviewed, focusing on their role in the development of the different gastric disorders, i.e. functional dyspepsia, gastric premalignant lesions (chronic atrophic gastritis, intestinal metaplasia and dysplasia of the gastric mucosa) and gastric cancer. Moreover, we focus on the effects on the gastric microbiota of exogenous interference as diet and use of proton pump inhibitors (PPIs).