To search for unique mutations in the apolipoprotein B (apoB) gene that disrupt the binding of LDL to its receptor and cause hypercholesterolemia, we examined more than 800 patients with high LDL cholesterol levels and/or coronary artery disease (CAD). Analysis of patient DNA by single-strand conformation polymorphism and allele-specific oligonucleotide hybridization of the sequence surrounding the putative receptor- binding domain of apoB (amino acid positions 2965 to 3534) revealed seven variations. LDL from heterozygotes with either Arg 3500 Gln or Arg 3531 Cys bound defectively with the LDL receptor in competitive binding assays. The Arg 3500 Gln substitution was statistically more prevalent in patients with hypercholesterolemia (P = 0.0003). Total cholesterol and LDL-cholesterol were significantly higher (P< 0.0004) in 34 apoB 3500 Gln carriers than in the controls. The allele encoding the Arg 3531 Cys substitution was more prevalent (0.8%) in the CAD group (P = 0.05) than in the controls. A Ser 3252 Gly variant was statistically more prevalent in the hypercholesterolemic group (P = 0.03), but LDL with this mutation had normal LDL receptor-binding activity. The other four variants identified (Leu 3350 Leu, Gln 3405 Glu, Val 3396 Met, and Ser 3455 Arg) were not associated with defective LDL-receptor binding, hypercholesterolemia, or CAD, nor were the apoB mutations associated with elevated lipid levels in family members. The surprising result that only two mutations of apoB in the receptor-binding domain (Arg 3500 Gln and Arg 3531 Cys) were associated with defective LDL binding, hypercholesterolemia, or CAD is in stark contrast with familial hypercholesterolemia, where nearly 150 mutations of the LDL receptor have been described that disrupt its function. This study strongly suggests that a limited number of mutations of apoB markedly influence LDL binding to its receptor.