Apolipoprotein (apo) C-II is a cofactor for lipoprotein lipase, the enzyme that catalyzes the hydrolysis of triglycerides on plasma triglyceride-rich lipoproteins. The complete coding sequence of apoC-II mRNA has been determined from an apoC-II clone isolated from a human liver cDNA library. A 17-base-long synthetic oligonucleotide based on amino acid residues 5-10 of apoC-II was utilized as a hybridization probe to select recombinant plasmids containing the apoC-II sequence. Two thousand four hundred clones were screened and one apoC-II cDNA clone containing 500 bases was identified. DNA sequence analysis of this clone revealed a 101 amino acid C-II apolipoprotein containing a 22 amino acid signal peptide attached to the amino terminus of the 79 amino acid residue plasma apoC-II. The amino acid sequence of apoC-II determined by nucleic acid analysis is in agreement with the recently determined sequence of plasma apoC-II isolated from normal subjects. The determination of the complete cDNA sequence of apoC-II and the availability of a cDNA probe of apoC-II will facilitate our analysis of the biosynthesis and processing as well as the genomic organization of apoC-II in normal subjects and patients with dyslipoproteinemias characterized by hypertriglyceridemia.