As optical sensors, single-walled carbon nanotubes (SWCNTs) have properties that make them ideally suited for detection of biologically important analytes. Carbon nanotubes exhibit band gap fluorescence which does not photobleach or blink, and their fluorescent properties can be modulated by changes in their immediate environment. Tissue transparent emission, biocompatibility, and versatile modes of optical response make SWCNTs uniquely valuable optical biosensors. Using these properties, we have rationally designed SWCNT-based sensors for enhanced quantification of biomarkers in biofluids for diagnostic applications and for the study of fundamental biological processes.