Implantable microelectrodes have the potential to become part of neural prostheses to restore lost nerve function after nerve damage. The initial adsorption of proteins to materials for implantable microelectrodes is an important factor in determining the longevity and stability of the implant. Once an implant is in the body, protein adsorption takes place almost instantly before the cells reach the surface of an implant. The aim of this study was to identify an optimum material for electrode recording sites on implantable microelectrodes. Common materials for electrode sites are gold, platinum, iridium, and indium tin oxide. These, along with a reference material (titanium), were investigated. The thickness and the structure of adsorbed proteins on these materials were measured using a combination of atomic force microscopy and ellipsometry. The adsorbed protein layers on gold (after 7 and 28 days of exposure to serum) were the smoothest and the thinnest compared to all the other substrate materials, indicating that gold is the material of choice for electrode recording sites on implantable microelectrodes. However, the results also show that indium tin oxide might also be a good choice for these applications.