The human and bovine forms of the hydrophobic 3.7 kDa surfactant polypeptide have been structurally analyzed. The polypeptide is essentially inert to enzymatic proteolysis, and methods for analysis include peptide handling in organic solvents and fragment generation by limited acid hydrolysis. The molecule exhibits N-terminal trimming, and the relative abundance of the different starting positions varies both among species and between adult and fetal forms of the surfactant polypeptide. The bovine major form is one residue shorter than the mature 35-residue human molecule. Comparison of the porcine, human and bovine polypeptides reveals a conserved hydrophobic middle/C-terminal segment and a variable hydrophilic N-terminal part.