Structural investigations of bare and surface-modified polystyrene microspheres (beads) have been carried out by infrared-visible sum frequency generation (SFG) vibrational spectroscopy and scanning force microscopy (SFM). Bead surfaces have been modified by either the covalent linking of immunoglobulin G (IgG) and bovine serum albumin (BSA) or the nonspecific adsorption of a Pluronic surfactant. After surface modification with protein, SFG signals in the aliphatic CH-stretch region are detected at both the buffer/bead and air/bead interfaces, indicating that some amino acid residues in proteins adopt preferred orientations. SFG results indicate that the hydrophobic poly(propylene glycol) moieties in the Pluronic order when adsorbed onto the bead, at both the buffer/bead and air/bead interfaces, whereas hydrophilic poly(ethylene glycol) groups align to a lesser extent. SFG spectra also show that the phenyl rings of bare polystyrene beads in contact with air or buffer are ordered, with a dipole component directed along the surface normal, but become less ordered after the adsorption of either proteins or the polymer. Molecular orientation and ordering at the bead surface affect its hydrophobicity and aggregation behavior. SFM results reveal the formation of nonuniform islands when bare beads with more hydrophobic character are spun-cast onto a silica substrate. In the presence of adsorbed protein, a hexagonal packing of beads, with some defects, is observed, depending on the bulk pH and the type of attached protein. Adsorbed Pluronic causes the beads to aggregate in a disordered fashion, as compared to the behavior of bare and protein-modified beads.