To seek apolipoprotein B (apoB) gene mutations in children and adolescents presenting to a lipid clinic with hypercholesterolemia and suspected of familial defective apoB (FDB), employing a new automated denaturing high performance liquid chromatography (DHPLC) method.131 patients between the ages of 3 and 18 years were screened for the presence of FDB mutations using DHPLC. Patients who exhibited aberrant DHPLC chromatograms were sequenced.Three patients were found to be positive for the R3500Q mutation in which a single nucleotide G-->A transition resulted in arginine to glutamine substitution at codon 3500 in exon 26 of the apoB-100 gene. All three subjects had elevated total cholesterol and LDL cholesterol levels, and high or borderline high plasma apoB levels. No R3500W or R3531C apoB mutations were found.Automated DHPLC can be readily applied in rapid screening of hypercholesterolemic children presenting to a lipid clinic. Using DHPLC, this study revealed that the FDB mutation (R3500Q) is an important contributing factor to hypercholesterolemia observed in a pediatric lipid clinic population.