Apolipoprotein C-III (apoC-III) is a major protein component of very low density lipoproteins (VLDL), chylomicrons, and a minor component of high density lipoproteins (HDL). Studies of naturally occurring human variants of apoC-III will help in adding to our understanding of the physiological function of this apolipoprotein. Using isoelectric focusing (IEF) of VLDL fractions we screened over 2500 lipid clinic patients and have identified an individual with a novel apoC-III variant. DNA sequencing revealed the variant to be a Lys for GIn exchange at amino acid residue 38 due to an A for C substitution in exon 3. This was confirmed by NH2-terminal protein sequence analysis. The mutant Lys38 variant was present in VLDL at about the same level as the normal form although the total amount of apoC-III was increased by 34%. The proband, a 16-year-old boy of Mexican origin, had a plasma level of total triglycerides above the 95th percentile for his age. Family studies revealed a further 16 individuals who were heterozygous for this apoC-III (Gln38-->Lys) variant. Compared to 21 unaffected relatives, the 17 heterozygous subjects had a statistically significant 32% elevation of their plasma levels of triglycerides when adjusted for age, sex, body mass index, and lifestyle. Other lipid and lipoprotein values were unaffected. The presence of an additional positive charge at residue 38 suggests that this residue is involved in the function of apoC-III. The elevation of plasma levels of triglycerides supports the view that apoC-III is involved in the regulation of the catabolism of triglyceride-rich lipoproteins.