Proteins have been conjugated to carbon nanotubes for applications in biosensing, biorecognition, delivery, and functional composites. Despite the growing interest in these carbon nanotube-protein hybrids, very little is known about how carbon nanotubes affect the structure and function of bound proteins. Here we provide an overview of our recent efforts to gain a more fundamental understanding of how proteins interact with carbon nanotubes. We also discuss recent results from our laboratories which suggest several new opportunities for protein-carbon nanotube conjugates to address problems in materials science and biotechnology.