Polyzwitterions (PZs), such as carboxybetaine and phosphobetaine polymers, show remarkable suppression of protein adsorption and have potentially widespread application as bioengineering materials. We show that free energy profiles, from molecular dynamics simulations in explicit water, for hydrophilic and hydrophobic amino acids approaching a PZ monomer, provide thermodynamic insights into protein adsorption. The predicted profiles for PZ have almost no energetically stable points, regardless of the type of residue. In contrast, the profiles for conventional polyester show some energetically remarkable minima, particularly for the hydrophobic residue. These results agree with recent experimental reports of differences in the amounts of protein adsorbed on these polymers, suggesting that free energy calculations for hydrophobic residue can play a significant role in assessing antifouling properties. Our simple strategy, which investigates the affinities between residues and monomers, can become a convenient approach to predicting protein antifouling properties of polymeric materials. © 2012 American Chemical Society.