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Carbon nanotubes (CNTs) have a great potential for applications in medicine. However, their biocompatibility and toxicity cause a great concern. Due to the large surface area of CNTs, chemical modification can dramatically alter their physiochemical properties and hence biological activity. Using a combinatorial chemistry approach, we report the synthesis of an 80-member surface-modified nanotube library. Based upon screening of this library with respect to protein-binding capacity, cytotoxicity, and immune response, we were able to select highly biocompatible nanotubes with reduced protein-binding cytotoxicity and immune response.