We have developed a high throughput method for prototyping discrete library substrates for rapid cytotoxicity and other cell-based screening of biomaterials. Surface-erodible polyanhydrides have been studied as carriers for drugs, proteins, and vaccines. The polyanhydrides in this work were based on sebacic acid (SA), 1,6-bis(p-carboxyphenoxyhexane) (CPH), and 1,8-bis(p-carboxyphenoxy)-3,6-dioxaoctane (CPTEG) copolymers. Within a few hours we designed, fabricated, synthesized, and characterized a linearly varying compositional library of 25 different polyanhydride random copolymers (based on CPH:SA and CPTEG:CPH) using discrete (organic-solvent resistant) multi-sample substrates created with a novel rapid prototyping method. We have validated this methodology with NMR and GPC characterization of the library. The discrete library was rapidly screened with standard myeloma, epithelial, and macrophage cell lines and was found to have no pronounced cytotoxic effect for any CPH:SA or CPTEG:CPH composition at a concentration higher than that expected in biomedical applications. These results add to the large body of evidence supporting the use of polyanhydrides as biocompatible materials for use in drug delivery devices. Further, we evaluated activation of immune cells such as bone marrow derived dendritic cells by screening the polyanhydride libraries and quantified the role of polymer chemistry in affecting the immune response. This was performed by measurements of cell surface markers and cytokines. The methodologies we have described are amenable to numerous applications in the arena of high-throughput biomaterials synthesis and characterization and will enable rapid and rational design of biomaterials.