Controlling protein adsorption on polymeric surfaces is one of the major challenges for developing novel biomaterials. To clarify microscopic mechanisms on the suppression of protein adsorption, identification of crucial factors for achieving excellent biocompatibility is significant. In this study, free energy calculations are introduced to assess the biocompatibility of two types of material: poly(2-hydroxyethyl methacrylate) (PHEMA) and poly(vinyl alcohol) (PVA). Free energy profiles are evaluated for an amino acid residue approaching their repeat unit in explicit water molecules from molecular dynamics simulations. Although PHEMA and PVA are generally both hydrophilic, the predicted profiles become remarkably different from each other. The profile for PHEMA shows nearly flat profiles, while the profile for PVA shows energetically stable minimum. These results theoretically demonstrate that hydrophilicity is not a crucial factor for achieving excellent biocompatibility, although it can be a prerequisite.