Background: Mutations in the dra gene result in congenital chloride diarrhoea (CLD) which is characterized by secretory diarrhoea, loss of Cl- in the stool, dehydration and metabolic alkalosis. These patients also have a higher risk of incidence of acute as well chronic intestinal inflammation. The slc26a3 (dra) deficient mice mimic the features and symptoms observed in CLD patients, but it is unknown whether they also display the propensity for intestinal inflammation. Aim: The present study was undertaken to explore whether the slc26a3-/- mice develop spontaneous intestinal inflammation, and if an altered epithelial barrier function and/or microbiome composition may be the underlying molecular mechanism for inflammation. Methods: Slc26a3-/- and wt littermates were studied from week 5-20 after birth. Stool water and Lipocalin2 (intestinal inflammation marker) were assayed weekly. After sacrifice at the designated time points, the inflammatory state of the mucosa was assessed by qPCR and immunohistochemistry. Mucus production and composition was assessed by histochemical staining of the mucins. The luminal and the mucosa-adherent colonic microbiome was assessed by 16S rRNA sequencing, and the effect of the microbiome of the slc26a3-/- colon on the development of inflammation in germ free mice by fecal crossing experiments. Results: In the slc26a3-/- mice, stool water content was increased (Weeks 4- 7; n= 9 pairs; p <0.0037, weeks 8-11; n= 9 pairs; p <0.0003, weeks 12-15; n= 9 pairs; p <0.0009, weeks 16-20; n= 7 pairs; p <0.0002). Qualitatively, immunohistochemistry of muc2 revealed a significant reduction in the goblet cells with a shift being observed towards the acidic mucins (n=3 pairs/time point). The luminal microbiome was dysbiotic from the earliest measurable time point with dramatically reduced microbiome diversity (n=5 pairs/time point). Over time, the slc26a3-/- mice developed mild colonic inflammation as evidenced by an increase in the stool lipocalin2 levels (n=5 pairs, p<0.05) and an increase in the mRNA levels of Ly6g, a neutrophil marker (Weeks 11-15, n= 16 pairs; p = 0.0070, weeks 17- 21, n= 13 pairs, p = 0.0003). The differences in microbiome composition partially persisted after transfer into germfree mice. However they did not develop intestinal inflammation and displayed an increase in the microbiome diversity. Conclusions: Slc26a3-/- mice display very low colonic pH microclimate, disturbances in mucin production and mucus barrier properties, strongly reduced microbiome diversity, and some of the slc26a3-/- mice develop overt colonic inflammation. Similar events may occur in the gut of CLD patients.