5-HT3 receptors are members of the Cys-loop superfamily of ligand-gated ion channels. In both the central and the peripheral nervous systems, 5-HT3 receptors excite postsynaptic cells and modulate the release of neurotransmitters from presynaptic neurons. 5-HT3 receptors are known to be involved in mediation of nausea/emesis caused by chemo/radio-therapy and anaesthesia, and more recently have also been found to be involved in irritable bowel syndrome. 5-HT3 receptors have also been suggested to play a role in a range of other indications, including various psychiatric disorders. This review summarizes the current evidence for the contribution of 5-HT3 subunit genes to disease phenotypes arising from association studies. Furthermore, it suggests how in vitro characterization of naturally occurring genetic variants can be used to obtain a better understanding of the causal relationship between gene and disease.