We have developed a novel method to study the influence of surface nanotopography on human fibrinogen adsorption at a given surface chemistry. Well-ordered arrays of nanoholes with different diameters down to 45 nm and a depth of 50 nm were fabricated in silicon by electron beam lithography and reactive ion etching. The nanostructured chip was used as a model system to understand the effect of size of the nanoholes on fibrinogen adsorption. Fluorescence imaging, using the intrinsic fluorescence of proteins, was used to characterize the effect of the nanoholes on fibrinogen adsorption. Atomic force microscopy was used as a complementary technique for further characterization of the interaction. The results demonstrate that as the size of the nanoholes is reduced to 45 nm, fibrinogen adsorption is significantly increased.