We describe a gel isoelectric focusing procedure for resolving into at least five bands the arginine-rich protein of very-low-density lipoproteins, and use the method in diagnosis of hyperlipoproteinemia type 3. We find that deficiency of one band, designated E3, relative to E2, expressed as an E3/E2 ratio less than or equal to 0.3, is specifically associated with hyperlipoproteinemia type 3 as diagnosed by traditional criteria in a large family study. In addition, we used the procedure to test 47 referral samples with demonstrable beta-migrating very-low-density liproprotein grouped by very-low-density lipoprotein cholesterol/total triglyceride ratios of greater than or equal to 0.3, from 0.25 to 0.3, and less than 0.25. All 24 of the first group, three of six in the second, and only one of 17 in the third had E3/E2 ratios of less than or equal to 0.3. Also, two normolipidemic children, without detectable lipoprotein abnormalities but related to subjects with hyperlipoproteinemia type 3, had E3/E2 ratios of less than or equal to 0.3. Use of our procedure improves the specificity of diagnosis and allows sensitive detection of asymptomatic subjects who may be at risk of developing the disorder.