Familial hypercholesterolemia (FH) and familial defective apoB 100 (FDB) are characterized by increased plasma low-density lipoprotein cholesterol (LDLc) levels and risk of coronary heart disease (CHD). FDB is clinically indistinguishable from FH. The aims of this study were to evaluate clinical diagnosis criteria for FDB and to compare the lipoprotein phenotype between carriers of LDL receptor (LDLR) gene mutations that affect the ligand-binding domain and subjects with the R3500Q mutation in apoB gene. We studied 213 subjects (113 probands) with FH and 19 heterozygous FDB subjects. Genetic diagnosis was determined by following a protocol based on Southern blot and polymerase chain reaction-single strand conformation polymorphism (SSCP) analysis. Thirty FH carriers of LDLR gene missense mutations that affect ligand-binding domain were matched by age, gender, and body mass index to the 19 FDB subjects (R3500Q mutation). Lipoprotein phenotype comparison was conducted between the 2 groups. FH patients showed plasma total and LDL cholesterol levels significantly higher than those in FDB patients. Three FDB showed plasma total and LDLc values in the normal range. Using the 1999 clinical Med-Ped criteria for diagnosis of genetic hypercholesterolemia, no FDB subjects had a confirmed diagnosis; it was probable in 36% of the subjects, it was possible in 32% of the subjects, and it could be excluded in the remaining 32% of the subjects. We conclude that the FDB lipoprotein phenotype was significantly less severe than that observed in FH carriers of LDLR gene missense ligand-binding domain mutations. Clinical Med-Ped diagnosis criteria tend to under-diagnose FDB.