Krul et al. (1) have identified two truncated species of apolipoprotein B-100 in a kindred with familial hypobetalipoproteinemia. Five family members were identified who produce either one or both of two truncated apolipoprotein B-100 proteins estimated to be 40% and 90% the amino-terminal end of apolipoprotein B-100. Low density lipoprotein with the apolipoprotein B-90 binds more strongly to the low density lipoprotein-receptor on cultured fibroblasts. In this present study, we have identified the DNA mutations leading to these truncated apolipoprotein B-100 variants in this kindred. Sequencing of amplified DNA from the proband revealed that deletions of one or two nucleotide bases produced frameshift mutations and generated premature stop codons in both cases. Apolipoprotein B-40 (Val1829----Cys-TERM) is the result of a dinucleotide (TG) deletion in exon 26 that generates a stop codon at position 1830 and produces a protein with a predicted molecular mass of 207.14 kDa. The other truncated apolipoprotein B Glu4034----Arg-Gln-Leu-Leu-Ala-Cys-TERM) is due to a single nucleotide (G) deletion in exon 29. This results in a protein with 4039 amino acids and a predicted molecular mass of 457.6 kDa that is now designated apolipoprotein B-89. Mechanisms by which the removal of the last 497 amino acids might increase the binding of the apoB-89 to the LDL-receptor are discussed.