We report on the fabrication and characterization of fully organometallic multilayer thin films, composed of poly(ferrocenylsilane) polyanions and polycations. These polyions were deposited electrostatically onto a variety of substrates including quartz, silicon, gold, and hydrophilic/hydrophobically patterned substrates, using layer-by-layer self-assembly. The deposition process was monitored by means of UV/visible absorption spectroscopy, showing a linear increase in absorption with the number of bilayers. Ellipsometry was used to measure the development of film thickness with the number of bilayers, revealing a linear relationship and a thickness contribution of approximately 0.4 nm/bilayer. The multilayer films were further characterized by X-ray photoelectron spectroscopy (XPS) and by cyclic voltammetry. By integration of the voltammetric signals, the surface concentration of the redox-active ferrocene units was obtained as a function of the number of poly(ferrocenylsilane) bilayers. Selective adsorption of the polyions was achieved onto the hydrophobic stripes of a pattern of CH3- and OH-terminated alkanethiol monolayers on gold, forming patterned organometallic multilayer structures. This selective deposition was explained by taking hydrophobic and hydrogen-bonding interactions into account. The hydrophobic backbone of the poly(ferrocenylsilane) polyions has favorable hydrophobic interactions with the methyl-terminated areas of the patterned substrate but not with hydroxyl-terminated domains, which are hydrogen-bonded with the solvent. The dipping sequence does not influence the selectivity of the multilayer deposition.