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Mutations in <i>APOB</i> are the second most frequent cause of familial hypercholesterolemia (FH). <i>APOB</i> is highly polymorphic, and many variants are benign or of uncertain significance, so functional analysis is necessary to ascertain their pathogenicity. Our aim was to identify and characterize <i>APOB</i> variants in patients with hypercholesterolemia. Index patients (<i>n</i> = 825) with clinically suspected FH were analyzed using next-generation sequencing. In total, 40% of the patients presented a variant in <i>LDLR</i>, <i>APOB</i>, <i>PCSK9</i> or <i>LDLRAP1</i>, with 12% of the variants in <i>APOB</i>. These variants showed frequencies in the general population lower than 0.5% and were classified as damaging and/or probably damaging by 3 or more predictors of pathogenicity. The variants <i>c.10030A>G</i>;p.(Lys3344Glu) and <i>c.11401T>A</i>;p.(Ser3801Thr) were characterized. The p.(Lys3344Glu) variant co-segregated with high low-density lipoprotein (LDL)-cholesterol in 2 families studied. LDL isolated from apoB p.(Lys3344Glu) heterozygous patients showed reduced ability to compete with fluorescently-labelled LDL for cellular binding and uptake compared with control LDL and was markedly deficient in supporting U937 cell proliferation. LDL that was carrying apoB p.(Ser3801Thr) was not defective in competing with control LDL for cellular binding and uptake. We conclude that the apoB p.(Lys3344Glu) variant is defective in the interaction with the LDL receptor and is causative of FH, whereas the apoB p.(Ser3801Thr) variant is benign.