In recent years there has been evidence of a significant link between autism and gastrointestinal (GI) disturbances highlighting the existence of a so-called “gut-brain axis.” This hypothesis asserts that GI abnormalities could trigger neuropsychiatric symptoms. Intestinal microbiota is thought to play a pivotal role in gut and systemic homeostasis, in central nervous system development, neurotransmitter creation, and behavioral modulation. Recurrent microbial imbalances have been shown in gut microbiota of people with Autism. In this review we analyze current knowledge about intestinal microbiota and the relevance and role of dysbiosis in ASD. The most accredited theories about gut-brain interaction will be reviewed, along with current scientific evidence supporting the relationship between microbial imbalances and impairment of neurodevelopment.