Functional dyspepsia (FD) is a highly prevalent disorder of gut-brain interaction (DGBI), previously known as a functional gastrointestinal disorder. Characterized by early satiety, postprandial fullness, and/or epigastric pain or burning, diagnosis depends on positive symptomatology and exclusion of obvious structural diseases. A subtle inflammatory phenotype has been identified in FD patients, involving an increase in duodenal mucosal eosinophils, and imbalances in the duodenal gut microbiota. A dysregulated epithelial barrier has also been well described in FD and is thought to be a contributing factor to the low-grade duodenal inflammation observed, however the mechanisms underpinning this are poorly understood. One possible explanation is that alterations in the microbiota and increased immune cells can result in the activation of cellular stress response pathways to perpetuate epithelial barrier dysregulation. One such cellular response pathway involves the stabilization of hypoxia-inducible factors (HIF). HIF, a transcriptional protein involved in the cellular recognition and adaptation to hypoxia, has been identified as a critical component of various pathologies, from cancer to inflammatory bowel disease (IBD). While the contribution of HIF to subtle inflammation, such as that seen in FD, is unknown, HIF has been shown to have roles in regulating the inflammatory response, particularly the recruitment of eosinophils, as well as maintaining epithelial barrier structure and function. As such, we aim to review our present understanding of the involvement of eosinophils, barrier dysfunction, and the changes to the gut microbiota including the potential pathways and mechanisms of HIF in FD. A combination of PubMed searches using the Mesh terms functional dyspepsia, functional gastrointestinal disorders, disorders of gut-brain interaction, duodenal eosinophilia, barrier dysfunction, gut microbiota, gut dysbiosis, low-grade duodenal inflammation, hypoxia-inducible factors (or HIF), and/or intestinal inflammation were undertaken in the writing of this narrative review to ensure relevant literature was included. Given the findings from various sources of literature, we propose a novel hypothesis involving a potential role for HIF in the pathophysiological mechanisms underlying FD., Competing Interests: SH declares no conflicts of interest. GB declares no conflicts of interest. EH declares no conflicts of interest. SK declares grant/research support from Cancer Institute NSW (Career Development Fellowship), National Health and Medical Research Council (Center of Research Excellence, Project and Ideas Grant), Viscera Labs, Gossamer Bio, Anatara Lifesciences, Microba (Funded research and consultancy). NT reports, non-financial support from HVN National Science Challenge NZ, personal fees from Aviro Health (Digestive health) (2019), Anatara Life Sciences, Brisbane (2019), Allakos (gastric eosinophilic disease) (2021), Bayer (IBS) (2020), Danone (Probiotic) (2018), Planet Innovation (Gas capsule IBS) (2020), Takeda, Japan (gastroparesis) (2019), twoXAR (2019) (IBS drugs), Viscera Labs, (USA 2021) (IBS-diarrhea), Dr Falk Pharma (2020) (EoE), Censa, Wellesley MA USA (2019) (Diabetic gastroparesis), Cadila PharmIncaceuticals (CME) (2019), Progenity Inc. San Diego, (USA 2019) (Intestinal capsule), Sanofi-aventis, Sydney (2019) (Probiotic), Glutagen (2020) (Celiac disease), ARENA Pharmaceuticals (2019) (Abdominal pain), IsoThrive (2021) (esophageal microbiome), BluMaiden (2021), Rose Pharma (2021), Intrinsic Medicine (2021), Comvita Mānuka Honey (2021) outside the submitted work; In addition, NT has a patent Nepean Dyspepsia Index (NDI) 1998, Biomarkers of IBS licensed, a patent Licensing Questionnaires Talley Bowel Disease Questionnaire licensed to Mayo/Talley, a patent Nestec European Patent licensed, and a patent Singapore Provisional Patent “Microbiota Modulation Of BDNF Tissue Repair Pathway” issued, “Diagnostic marker for functional gastrointestinal disorders” Australian Provisional Patent Application 2021901692. Committees: OzSage, Australian Medical Council (AMC) [Council Member]; Australian Telehealth Integration Programme; MBS Review Taskforce; NHMRC Principal Committee (Research Committee) Asia Pacific Association of Medical Journal Editors. Boards: GESA Board Member, Sax Institute, Committees of the Presidents of Medical Colleges. Community group: Advisory Board, IFFGD (International Foundation for Functional GI Disorders), AusEE. Miscellaneous: Avant Foundation (judging of research grants). Editorial: Medical Journal of Australia (Editor in Chief), Up to Date (Section Editor), Precision and Future Medicine, Sungkyunkwan University School of Medicine, South Korea, Med (Journal of Cell Press). NT is supported by funding from the National Health and Medical Research Council (NHMRC) to the Center for Research Excellence in Digestive Health and he holds an NHMRC Investigator grant., (Copyright © 2022 Hari, Burns, Hoedt, Keely and Talley.)