The gene structure of the human 5-HT3A receptor gene was analyzed by exon to exon polymerase chain reaction and subsequent sequencing. The results were confirmed by restriction analysis and genomic Southern blotting. The coding region of the human gene was found to be split by eight introns at identical positions as in the murine 5-HT3A receptor gene. All exon-intron boundaries exhibited fully conserved splice donor and acceptor consensus sequences. The alternative splice acceptor in intron eight of the murine gene was not found in the human counterpart. The length of particular introns differs markedly from the murine gene. With the exception of intron 5, all human introns are longer than their murine counterparts. From the start to the stop codon the human gene stretches over about 14.5 kb. The human exon sequences confirm one of three published human 5-HT3A receptor cDNA sequences. Knowledge of the gene structure, including 1.9 kb of the 5' noncoding region, all introns and the exon-intron boundaries of the human 5-HT3A receptor gene should facilitate investigation of its potential role in psychiatric disorders.