Apolipoprotein B occurs in the plasma in 2 main isoforms, APOB48 and APOB100. The first is synthesized exclusively by the small intestine, the second by the liver. Both isoforms are coded by APOB and by a single mRNA transcript larger than 16 kb. APOB48 is generated when a stop codon (UAA) at residue 2153 is created by RNA editing. As a result of the RNA editing, APOB48 and APOB100 share a common N-terminal sequence, but APOB48 lacks APOB100's C-terminal LDL receptor binding region. In fact, APOB48 is so called because it constitutes 48% of the sequence for APOB100.

APOB 48 is a unique protein to chylomicrons from the small intestine. After most of the lipids in the chylomicron have been digested, APOB48 returns to the liver as part of the chylomicron remnant, where it is endocytosed and degraded.