Human apolipoprotein (apo) A-IV is a polymorphic plasma protein controlled by two codominant alleles at a single genetic locus. Thus far, five different isoproteins (apoA-IV-0 to apoA-IV-4) have been described in Caucasians. We have recently identified the nucleotide and amino acid substitutions that are the basis for the most common isoproteins, apoA-IV-1 and apoA-IV-2. In this report, the mutations producing the two rare isoproteins apoA-IV-0 and apoA-IV-3 are described. Analysis of the apoA-IV-0 allele revealed an insertion of 12 nucleotides in a carboxyl-terminal region, which is highly conserved among human, rat, and mouse A-IV apolipoproteins. This in-frame insertion of the 4 amino acids Glu-Gln-Gln-Gln between residues 361 and 362 of the mature protein produces the 1 charge unit more acidic apoA-IV-0 isoprotein (pI 4.92). In the apoA-IV-3 allele we identified a single G to A substitution that converts the glutamic acid (GAG) at position 230 of the mature protein to a lysine (AAG), thus adding 2 positive charge units to the apoA-IV-1 isoprotein (pI 4.97) and forming the more basic apoA-IV-3 isoprotein (pI 5.08). Comparison with the mouse and rat A-IV apolipoproteins revealed that this residue, located at position 4 of the 10th/11th amphiphilic alpha-helical repeat, is also highly conserved in evolution.