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Introduction: Very little is known about the variation in the mucosa-associated microbiota (MAM) along the human gastrointestinal (GI) tract. We aimed to determine the biogeography of the MAM along the GI tract of subjects without identifiable gastrointestinal disease, and in comparison, with Crohn's disease (CD) and Ulcerative colitis (UC) patients. Methods: Biopsies from the duodenum (DU), terminal ileum (TI), ascending colon (RC) and rectum (R) from 21 “asymptomatic control” subjects, (i.e. referred for diagnostic work-up following a positive faecal occult blood test), and 37 inflammatory bowel disease (IBD) patients (30 with UC and 7 with CD) were collected using the Brisbane aseptic biopsy device and total DNA was extracted and the 16S ribosomal RNA gene amplicon libraries were sequenced using the Illumina MiSeq platform and the quality-filtered data were processed using the Quantitative Insights into Microbial Ecology version 2 (QIIME2) software, various R packages (including Phyloseq, edgeR, and ggplot2). Bacterial load on duodenal tissue was assessed and normalised to human DNA in each sample by qPCR, using Bacteria-domain 16S rRNA gene-specific primers, and primers targeting the human beta-actin gene. Results: Compared to the control subject group, the Shannon diversity for both IBD groups was reduced at the DU and RC, and specifically, at the TI for CD patients (P