Background The serotonin [5-hydroxytryptamine (5-HT)]-gated ion channel 5-HT3 is involved in the mediation of postoperative and radiotherapy/chemotherapy-induced nausea/emesis and in irritable bowel syndrome. It has also been suggested to play a role in various psychiatric diseases. Five naturally occurring single nucleotide polymorphisms leading to amino acid changes have been identified in the human 5-HT3A gene. Methods and results We investigated the functional effects of these polymorphisms on the 5-HT3A receptor using fluorescence-based cellular assays. Notably, variants A33T, S253N, and M257I displayed 5-HT-induced maximal responses of 3-64% of the wild-type response, whereas R344H and P391R exhibited wild-type-like function. All variants displayed wild-type-like potencies of 5-HT and three 5-HT3 antagonists. Furthermore, all variants displayed K-d values similar to that of the wild-type receptor in a [H-3]GR65630-binding assay. The surface expression of A33T, M2571, and R344H was reduced 2-4-fold compared with the wild-type, despite similar total expression levels. Finally, coexpression of wild-type 5-HT3A or 5-HT3B subunits with 5-HT3A variants A33T, S253N, or M257I resulted in mixed or heteromeric receptors, characterized by significantly reduced maximal responses to 5-HT compared with the wild-type receptors. Conclusions Three polymorphisms of the 5-HT3A gene gave rise to functionally impaired receptors whose function could not be rescued by either wild-type 5-HT3A or 5-HT3B. Three of the variant receptors were surface-expressed at reduced levels in spite of total expression levels similar to wild-type, indicating that these variants affect receptor biogenesis and/or trafficking. These severe single nucleotide polymorphism effects hold promise for identification of new 5-HT3A gene-disease causalities.