The method of thin film preparation known as layer-by-layer assembly is of growing interest for current and envisioned developments in bionanotechnology. Here, cysteine-containing 32mer peptides have been designed, synthesized, purified, and used to prepare polypeptide films. A range of methods-quartz crystal microbalance, Fourier transform infrared spectroscopy, circular dichroism spectroscopy, and high-performance liquid chromatography-have been used to probe the effect of ionic strength and polymer secondary structure in solution on peptide self-assembly, and on secondary structure formation and disulfide bond cross-linking in the multilayer film. The amount of designed peptide deposited per adsorption step of film fabrication increased with increasing ionic strength, as with conventional polyelectrolytes. Secondary structure content changed from random coil to beta sheet on incorporation of peptides into a film. "Peptide-inherent" cross-linking by disulfide bond formation increased film stability at acidic pH. Conditions for disulfide stabilization have been optimized. The results contribute to exploration of the physical basis of peptide self-assembly broaden the scope of applications of layer-by-layer assembly, particularly where biocompatibility and stability are key design concerns, and provide a basis for mass production of custom polypeptide thin films of high stability, even in harsh environments.