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Nanoparticles (NPs) are gaining increasing attention in the biomedical field because of their potential as biocatalysts, biosensors and drug delivery devices. In the human body, NPs rapidly interact with the blood plasma proteins and usually change the secondary structures of the proteins which subsequently dictates their biological responses, such as thrombogenesis (blood clotting). Previous studies have shown that size and shape of metal oxide NPs affect protein adsorption from whole blood plasma. Here, the adsorption of human serum albumin (HSA) and fibrinogen (Fg) on three types of titanium dioxide (TiO2, rutile)-hexagonal NPs (HNPs), nanotubes (NTs) and nanorods (NRs)-were investigated to study how shape and hydrophobicity affects protein adsorption and protein secondary structure. Hexagonal NPs were more hydrophobic than NTs or NRs. The order of the binding affinity obtained from adsorption isotherms for both proteins to the NPs was: HNPs > NTs > NRs. Fibrinogen had much higher binding affinity to all the NPs than HSA. The extent of α-helix loss of HSA adsorbed on the NPs was shape- and hydrophobicity-dependent. However, Fg showed similar structural changes on all three types of NPs probably due to its high binding affinity to all the NPs. These results indicate that surface hydrophobicity and shape of the NPs both have effects on the amount of proteins adsorbed, if the protein has a low affinity for the surface but proteins with high affinity for NP surfaces do not show shape- or hydrophobicity-dependent structural changes. The present results will give us insight into designing NPs that can prevent unfavorable biological responses such as thrombosis.