The gene for human apolipoprotein (apo) A-II has been isolated from a human genomic DNA library. The cloned fragment was approximately 14 kilobase-pair (kb) long, and extended about 9.0 kb upstream as well as 3.5 kb downstream from the apoA-II gene, which was contained within a 3.1 kb HindIII fragment of human DNA. The complete nucleic acid sequence of the apoA-II gene has been determined, establishing that the apoA-II gene is interrupted by three intervening sequences of 182, 293, and 395 bp. The second intron is of particular interest, because it contains a 33 bp sequence of alternating G and T residues very close to the 3' splice site which has the potential to form a left handed Z-helix structure in vivo. A restriction fragment length polymorphism 3' from the apoA-II gene has been detected which may serve as a marker for the long arm of chromosome 1 in linkage analyses.