There is increasing evidence that host-microbe interactions play a key role in maintaining homeostasis. Gut microbiota is essential to human health, playing a major role in the bidirectional communication between the gastrointestinal tract and the central nervous system. Recently, there is a growing interest of research on the relationship of gut-microbiota and neurological disorder. Accumulating data now indicate that the gut microbiota also comunicates with the CNS-possibly through neural, endocrine and immune pathways-and thereby influences brain function and behaviour. This review focuses on the importance of changed gut microbiota in behavioural and gastrointestinal manifestations and the significance of gut-brain axis in relation to the overall mental well-being in children with ASD. Of particular importance is the highlighting of some bioethical principles regarding the study of this subject.