The structure of the Drosophila melanogaster Antennapedia (Antp) gene has been investigated by the isolation and sequencing of different cDNAs and genomic clones. Northern analysis, S1 mapping and primer extension experiments reveal a complex and unusual gene structure. The gene is composed of two promoters, eight exons spanning >100 kb, and two termination processing regions. Four major polyadenylated transcripts were found, two of them starting at a second internal promoter in front of exon 3. All four transcripts have extremely long untranslated leader and trailer sequences in the range of 1-2 kb. Despite the complex transcriptional organization, the open reading frame is the same in all transcripts, and starts in exon 5 giving rise to a protein of mol. wt. 42 800. The putative protein is rich in glutamine (18%) and proline (10%). The homeobox, a region which previously has been shown to be highly conserved among homeotic genes, is contained in the open reading frame and located in the last exon. Functional implications of the complex structure with respect to development and its relation to the mutant phenotypes are discussed.