The invention offers an early detection method for atherosclerosis using genetic analysis to detect a polymorphisms shown to be correlated with this disease which are proximal to the apolipoprotein AI (apoAI) and aplipoprotein CIII (apoCIII) gene complex. All individuals with a 300 bp deletion 4 kb upstream of the apoAI gene are destined to experience severe atherosclerotic symptomologies. Individuals with a polymorphism 5.4 kb 5' of the apoAI gene or a PvuII polymorphism in the first intron of the apoCIII gene also seem to be at greater risk. A haplotype with MspI and XmnI/7.2 polymorphisms in this general region seem to be protected. Additional polymorphic sites in the DNA sequence associated with the apoAI/CIII gene complex provide a means for genetically fingerprinting individuals, and for identifying persons at risk with respect to disorders relating to lipid metabolism and transport.