Disulfides are chemically and electrochemically reactive functional groups that could be useful for ultra-high-resolution patterning of self-assembled monolayer films (SAMs) by atomic force microscopic (AFM) anodization. Zirconium-organophosphonate monolayers that contain embedded disulfide bonds were prepared by sequential deposition of Zr4+ and H2PO3-S-S-R components. Bis(10-phosphodecyl) disulfide and 10-phosphodecyldodecyl disulfide form monolayers on zirconated Si(100) and gold surfaces. X-ray photoelectron spectroscopy (XPS), AFM, contact angles, and ellipsometry were used to characterize these self-assembled films. The growth process is sluggish, and contact angle measurements suggest that the hydrocarbon chains in the film are disordered. The origin of these effects appears to be the preferred C-S-S-C dihedral angle of about 90degrees. Silicon substrates that have a thin native silicon oxide give a plasmon band in the XPS spectra, which can be mistaken for oxidized sulfur; we discuss a strategy for eliminating this interference. The disulfide groups embedded in these monolayers retain their chemical reactivity. On silicon substrates, dithiothreitol (DTT) readily cleaves the embedded disulfide bonds, leaving a thiol-terminated surface. However, on gold substrates, DTT also cleaves the Au-S bond and strips the monolayer from the gold. AFM anodization gave high-resolution patterning of the well-ordered methyl-terminated C 12 monophosphonate, but the methyl-terminated 10-phosphonodecyl dodecyl disulfide SAMs on native silicon oxide were too disordered and the underlying silicon was oxidized too.