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Neurofibromatosis type 1 (NF1) is a genetic condition presenting with variable symptomatology, however most individuals will demonstrate cognitive and behavioural difficulties, including autism. Using a heterozygous germline knockout mouse model of NF1 (Nf1 +/-), we performed in-depth behavioural evaluations encompassing learning and memory, stereotypy, social interaction, anxiety- and depression-like behaviour. Anatomical and functional studies of the brain and gastrointestinal tract were followed by the first investigation of gut microbiota composition (via full-length 16S rRNA sequencing) in a Nf1 +/- mouse model. The cognitive and autism-like behavioural phenotype seen in Nf1 +/- mice was accompanied by a striking increase in relative brain size which is highly relevant to clinical NF1. Furthermore, brain size was correlated with behaviour, supporting a potential mechanistic link. Nf1 +/- mice showed significant alterations in gut microbiota composition vs. Nf1 +/+ wild-type controls, with males additionally showing significant changes to species abundance of the Clostridium and Blautia genera, and the Lachnospiraceae family, findings which partially overlap with those in preclinical and clinical autism. Composition of associated functional pathways was not globally altered, however +/- mice showed significant changes in a pyrimidine deoxynucleotide biosynthesis pathway. In male Nf1 +/- mice, we also identified a genotype-specific host-microbial signature, pointing towards a mechanistic link between gut microbiome composition and brain size. These findings significantly expand our understanding of brain and behavioural abnormalities in this preclinical model of NF1 and, importantly, have uncovered the gut microbiome as a highly promising new area of research and a potential therapeutic target for these symptom clusters.