To evaluate the influence of substratum surface characteristics on protein adsorption processes, we have investigated the adsorption (adsorbed amount, supramolecular organization) of collagen on model substrata exhibiting controlled topography and surface chemistry. Substrata were prepared in two steps: (i) gold deposition onto silicon wafers (smooth substrata) and onto a support with nanoscale protrusions created by colloidal lithography (rough substrata); (ii) functionalization with CH3 (hydrophobic) and OH (hydrophilic) groups, using alkanethiol self-assembly. Atomic force microscopy (AFM) images were recorded under water, prior to and after collagen adsorption, and the images were analyzed quantitatively using two independent approaches. On smooth substrata, collagen formed a similar to6 nm thick, homogeneous layer with low roughness on hydrophilic surfaces, and a similar to20 nm thick layer exhibiting elongated aggregated structures on hydrophobic surfaces. Film thickness measurements (AFM) together with X-ray photoelectron spectroscopy (XPS) revealed larger adsorbed amounts on hydrophobic surfaces compared to hydrophilic ones. On rough substrata, the adsorbed amounts were similar to those found on smooth substrata; however, the collagen molecules no longer formed aggregated structures on the hydrophobic surfaces. It is concluded that while the adsorbed amount is only affected by the surface chemistry, the supramolecular organization of the adsorbed layer is controlled both by surface chemistry and topography. The approach presented here will have great value in biophysics for investigating bioadsorption and bioadhesion processes on substrata of defined surface properties.