There is evidence to suggest that genetic factors contribute to the manifestation of functional gastrointestinal disorders (FGID). As such, it is important to note that FGID are heterogeneous; they have quite different clinical features and (probably) different underlying pathophysiologic mechanisms. Evidence from family and twin studies indicates that there is clustering of FGID in families and increased concordance in monozygotic compared with dizygotic twins. The clinical features of FGID implicate polymorphisms in the genes that encode adrenergic, opioidergic or serotonergic receptors, as well as in the G-protein beta3 subunit (GNB3) gene and serotonin-transporter genes, in their manifestations. As mediators or regulators of mucosal inflammation can trigger events that ultimately result in manifestations of FGID, polymorphisms in genes that encode proteins with immunomodulatory and/or neuromodulatory features (e.g. OPRM1, IL4, IL4R, TNF) might also have a role in the manifestation of FGID. A two-step model for the role of genetic factors in the manifestation of functional gastrointestinal pain can, therefore, be proposed. In the presence of specific hereditary factors, environmental factors that do not usually cause long-term functional alterations are linked to the manifestation of symptoms.