Introduction Autism spectrum disorders (ASD) are characterized by deficient social interaction. Moreover, epidemiological data indicate that children and adults with ASD display marked gastrointestinal (GI) comorbidities and some evidence of altered microbial composition in the GI tract. Intriguingly, preclinical research has demonstrated that interventions to the gut microbiome can reverse both autism-like behaviour symptoms and GI abnormalities in animals. In conjunction, these findings suggest that miscommunication within the microbiome-gut-brain axis can contribute to the manifestation of ASD. The BTBR T+ Itpr3tf/J mouse, a well-known animal model of ASD, exhibits a robust deficit in sociability. However, there is limited information on the gut-brain signalling in this model of ASD. Methods BTBR and C57BL/6 adult male mice (n=10) were subjected to a battery of behavioural tests. To estimate changes in the gut motility, we analysed intestinal transit time with Carmin Red dye in vivo, as well as faecal water contents and colon length. To examine intestinal permeability, 4kDa FITC-dextran flux was analysed in distal ileum segments in Ussing chambers ex vivo. Ileum and colonic tissues were collected to measure tight junction proteins and serotonin-associated gene expression levels (qPCR), as well as serotonin contents (HPLC). Caecal microbiota composition was analysed by Illumina MiSeq. Data (mean±SEM) were compared by unpaired t-test; a p value <0.05 was deemed significant in all cases. Results BTBR mice showed more stereotyped behaviours in the marble burying and grooming tests, as well as reduced sociability in the 3-chamber and resident-intruder tests. On the GI side, BTBR mice demonstrated a significant delay in whole intestinal transit time (262±4 vs 238±4min), increased colon length (86±1 vs 70±1mm), and decreased faecal water content (47±1 vs 52±2%). These indicatives of a deficit in intestinal propulsive activity were accompanied by altered expression of genes involved in gut serotonin turnover. The analysis of FITC mucosal-to-serosal flux in ileum tissue revealed dramatic increase in the epithelial permeability (14.0±2.2 vs 5.5±1.8μg FITC/h*cm2) in BTBR animals. BTBRs showed a significant decrease in microbiota diversity and Firmicutes/Bacteroidetes ratio. On-going work is aimed to explore the associations between changes in gut and brain function and alterations in the gut microbial consortium. Conclusion Here we demonstrate that in BTBR mice autistic-like behaviours are associated with significant GI malfunction, which compromises such keystones of gut health as the integrity of intestinal barrier function and peristalsis. Our findings support the implication of the gut-brain axis paradigm in autistic disorders. The study is supported by Science Foundation Ireland (SFI) through the Irish Government’s National Development Plan (12/RC/2273).