When encapsulating proteins in polymer microspheres for sustained drug delivery there are three stages during which the stability of the protein must be maintained: (1) the fabrication of the microspheres, (2) the storage of the microspheres, and (3) the release of the encapsulated protein. This study focuses on the effects of polymer degradation products on the primary, secondary, and tertiary structure of tetanus toxoid, ovalbumin (Ova), and lysozyme after incubation for 0 or 20 days in the presence of ester (lactic acid and glycolic acid) and anhydride (sebacic acid and 1,6-bis(p-carboxyphenoxy)hexane) monomers. The structure and antigenicity or enzymatic activity of each protein in the presence of each monomer was quantified. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis, circular dichroism, and fluorescence spectroscopy were used to assess/evaluate the primary, secondary, and tertiary structures of the proteins, respectively. Enzyme-linked immunosorbent assay was used to measure changes in the antigenicity of tetanus toxoid and Ova and a fluorescence-based assay was used to determine the enzymatic activity of lysozyme. Tetanus toxoid was found to be the most stable in the presence of anhydride monomers, while Ova was most stable in the presence of sebacic acid, and lysozyme was stable when incubated with all of the monomers studied.