The neurotransmitter serotonin (5HT) has been implicated in morphogenesis of central nervous system and craniofacial structures. The actions of serotonin are mediated by multiple receptor subtypes, one of which, the 5HT3 receptor, is a ligand-gated ion channel. To determine whether this channel may contribute to the proposed morphogenic actions of serotonin, the expression of 5HT3 receptor transcripts was examined during mouse embryogenesis and correlated with the distribution of serotonin transporter mRNA and serotonin immunoreactivity. The pattern of 5HT3 receptor mRNA expression within the brain suggests possible roles for this receptor in the proliferation, differentiation, or migration of CNS neurons. In the peripheral nervous system, 5HT3 receptor transcripts were observed within cranial nerve sensory ganglia, olfactory neuroepithelia, and sympathoadrenal and enteric nervous systems during the initial stages of their formation. Striking expression of 5HT3 receptor transcripts occurred outside the nervous system, in association with regions of active chondrogenesis in the vertebral column, limbs, and craniofacial region, suggesting a possible involvement of this receptor subtype in the morphogenesis of olfactory receptor neurons, teeth, and genitalia.