Normal or disordered behaviour of the gastrointestinal tract is determined by a complex interplay between the epithelial barrier, immune cells, blood vessels, smooth muscle and intramurally located nerve elements. Mucosal mast cells (MMCs), which are able to detect noxious and antigenic threats and to generate or amplify signals to the other cells, are assigned a rather central position in this complex network. Signal input from MMCs to intrinsic enteric neurons is particularly crucial, because the enteric nervous system fulfils a pivotal role in the control of gastrointestinal functions. Activated enteric neurons are able to generate an alarm program involving alterations in motility and secretion. MMC signalling to extrinsic nerve fibres takes part in pathways generating visceral pain or extrinsic reflexes contributing to the disturbed motor and secretory function. Morphological and functional studies, especially studies concerning physiological stress, have provided evidence that, apart from the interaction between the enteric nervous system and MMCs, there is also a functional communication between the central nervous system and these mast cells. Psychological factors trigger neuronal pathways, which directly or indirectly affect MMCs. Further basic and clinical research will be needed to clarify in more detail whether basic patterns of this type of interactions are conserved between species including humans.