Over the last 10 years, the explosion of molecular biology and molecular genetic techniques have allowed major advances in the diagnosis and management of a wide variety of human disorders. These range from accurate and simple screening for carriers of thalassemia (Old JM, Varawalla NY, Weatherall DJ: Lancet 2:834-837, 1990) to the use of preimplantation diagnosis of embryos at risk for untreatable congenital defects (Monk M, Holding C: Lancet 1:985-988, 1990) and the development of gene therapy for treatment of disorders such as adenosine deaminase deficiency (Sharp D: Lancet 1:1277-1278, 1991). These same molecular techniques have also been applied to pediatric lipid disorders with some notable successes, both in their diagnosis and understanding the mechanisms of the resulting pathology, including the recent experiments (Wilson JM, Grossman M, Wu CH, Chowdhury NR, Wu GY, Chowdhury JR: J Biol Chem 267:963-967, 1992) that have led to proposals to treat homozygous familial hypercholesterolemia by gene therapy. The purpose of this review is to detail this molecular genetic progress for two of the disorders that result in disturbed triglyceride metabolism in infants, lipoprotein lipase deficiency and apo CII deficiency, and four disorders that lead to disturbed cholesterol levels in infancy, abetalipoproteinemia, hypobetalipoproteinemia, familial defective apo B, and familial hypercholesterolemia. We will also address the question of how knowledge of the mutation causing the defect in a particular patient could be clinically useful and highlight areas of research for the future.