The rat ATP-citrate lyase gene was cloned and the complete exon-intron organization of the gene has been identified. The ATP-citrate lyase gene, spanning about 55 kb, is divided into 29 exons that range in size from 30 to 986 base pairs. The sequences bordering the splice site junctions universally follow the GT/AG rule. Reverse transcription-polymerase chain reaction showed two forms of ACL mRNA; the one containing complete exons and the other lacking exon 14 were found in the brain, kidney, mammary gland, lung and liver. Also, the restriction fragment length polymorphisms were observed at intron 10 and intron 11 regions.