BDNF is a 13 kDa, 119 amino acid (aa) residue non-glycosylated polypeptide whose primary structure is conserved among all mammalian species examined. Initially synthesized as a 247 aa residue prepropeptide, the BDNF molecule is divided into an 18 aa residue signal sequence, a 110 aa residue prosequence, and a 119 aa residue mature segment.

Similar to other neurotrophic factors, there is a possibility that the N-terminus is alternatively spliced, giving rise to a longer pre-prosegment (but identical mature segment) with different functional properties. As a mature molecule, BDNF is 52% identical to NGF at the amino acid level, exists as a noncovalently-linked homodimer in solution, and contains six cysteine residues that are believed to form three intrachain disulfide linkages.