Layer-by-layer assembly of two palladium coordination-based multilayers on silicon and glass substrates is presented. The new assemblies consist of rigid-rod chromophores connected by terminal pyridine moieties to palladium centers. Both colloidal palladium and PdCl2(PhCN)2 were used in order to determine the effect of the metal complex precursor on multilayer structure and optical properties. The multilayers were formed by an iterative wet-chemical deposition process at room temperature in air on a siloxane-based template layer. Twelve consecutive deposition steps have been demonstrated resulting in structurally regular assemblies with an equal amount of chromophore and palladium added in each molecular bilayer. The optical intensity characteristics of the metal-organic films are clearly a function of the palladium precursor employed. The colloid-based system has a UV-vis absorption maximum an order of magnitude stronger than that of the PdCl2-based multilayer. The absorption maximum of the PdCl2-based film exhibits a significant red shift of 23 nm with the addition of 12 layers. Remarkably, the structure and physiochemical properties of the submicron scale PdCl2-based structures are determined by the configuration of the approximately 15 angstroms thick template layer. The refractive index of the PdCl2-based film was determined by spectroscopic ellipsometry. Well-defined three-dimensional structures, with a dimension of 5 microm, were obtained using photopatterned template monolayers. The properties and microstructure of the films were studied by UV-vis spectroscopy, spectroscopic ellipsometry, atomic force microscopy (AFM), X-ray reflectivity (XRR), scanning electron microscopy (SEM), and aqueous contact angle measurements (CA).