Apolipoprotein C-III (APO C-III) is a structural component of very-low-density and high-density lipoprotein particles and is an inhibitor of lipoprotein lipase. In a study of genetic variation of apolipoproteins in the Mayan population of the Yucatán peninsula, we observed a quantitative polymorphism in APO C-III levels. This polymorphism is expressed as variation in immunoblot staining intensity following isoelectric focusing and as variation in plasma levels of APO C-III determined by radial immunodiffusion. This variation is consistent with the presence in Mayans of an allele associated with low levels of plasma APO C-III which we have designated APO C-III*D. Analysis of the distribution of APO C-III levels yields a gene frequency estimate for the deficiency allele of 0.59. There is a significant positive correlation between total plasma APO C-III levels and total plasma cholesterol and triglyceride levels, the lowest levels of cholesterol and triglycerides being seen in individuals homozygous for the deficiency allele. This observation is consistent with the proposed role of APO C-III in lipoprotein metabolism. Family data to determine whether this deficiency allele is due to mutation at the APO C-III structural locus were not available. However, molecular analysis using cloned probes from the APO A-I/C-III/A-IV gene cluster revealed no gross DNA rearrangement or deletion of sequences in this region in homozygous deficient individuals.