The aim of this systematic review was to determine: 1. alternations of gut microbiota community; 2. intestinal barrier-related markers; 3. relationship between the intestinal ecosystem and health-related factors in AN individuals. We conducted a systematic literature search (PubMed/Embase/ClinicalTrials registry) until 30 September 2020 for studies reporting gut microbiome and intestinal barrier-related markers in patients with AN. Six studies on intestinal microbiota were eligible for this review, including three papers also describing intestinal barrier markers. Among five studies analyzing microbiota diversity, four of them found differences between AN patients and healthy controls (HC). The studies confirm alterations of the markers, which can affect intestinal barrier integrity of patients with ED. The systematic review confirms changes in the gut ecosystem of patients with eating disorder, without a clear consensus of microbiota patterns in AN. Damage of intestinal barrier integrity is poorly documented in AN patients and needs more attention in further studies.