Choline acetyltransferase (ChAT; acetyl-CoA:choline-O-acetyltransferase; EC 2.3.1.6) is the enzyme responsible for the synthesis of the neurotransmitter acetylcholine and is thus the genetic determinant of neurons with a cholinergic phenotype. We have screened a Drosophila genomic library using a cRNA probe, transcribed from Drosophila ChAT cDNA, and isolated three independent clones representing all the exons of this gene. The gene spans more than 26 kb of DNA and is organized into eight exons containing 594, 80, 192, 759, 408, 147, 201, and 1,612 nucleotides. All inserts that hybridized with a cRNA probe have been subcloned and the sequence of intron/exon boundaries determined. The only part of the ChAT gene not represented in our clones is a part of the first intron. A minimum size for this uncloned DNA has been deduced from Southern analysis of Drosophila genomic DNA. We also have probed the transcripts of the ChAT gene by northern analysis of total Drosophila RNA using two different exon-specific antisense RNA probes. An exon I probe detected two bands of RNA whereas an exon VIII probe hybridized with only the smaller band, previously identified as ChAT mRNA. These results indicate a complex transcription pattern for the ChAT locus in Drosophila.